Contacts of the helix formed by residues 122 - 143 (chain A) in PDB entry 3HL7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS 3.9 3.1 + - - +
121A LEU* 1.3 74.6 - - - +
123A ASP* 1.3 64.1 + - - +
124A ASP* 3.5 9.9 + - - +
125A HIS* 2.7 41.5 + - + +
126A VAL* 3.1 24.1 + - - +
216A LEU* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 1.3 73.4 - - - +
124A ASP* 1.3 62.2 + - - +
126A VAL* 3.3 7.5 + - - +
127A GLN* 2.9 38.6 + - - +
216A LEU* 3.8 14.7 - - + +
277A ASN* 2.9 42.2 + - - +
280A ALA* 4.3 0.2 - - - +
306A TYR* 2.7 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 3.1 9.8 + - - +
123A ASP* 1.3 80.2 - - - +
125A HIS* 1.3 63.6 + - + +
127A GLN* 3.4 14.7 + - - +
128A PHE* 3.3 16.6 + - - +
309A GLN* 3.6 20.2 + - - +
310A TYR* 3.8 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.3 15.9 - - + -
122A THR* 2.7 41.0 + - + +
124A ASP* 1.3 78.5 - - + +
126A VAL* 1.3 60.2 + - - +
128A PHE* 3.2 7.0 + - - +
129A LEU* 2.9 43.1 + - + +
161A CYS* 3.9 29.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.1 17.3 - - + +
122A THR 3.1 16.9 + - - +
123A ASP 3.7 5.4 - - - +
124A ASP 3.3 0.4 - - - -
125A HIS* 1.3 71.9 - - - +
127A GLN* 1.3 67.1 + - - +
129A LEU* 4.5 4.5 - - - +
130A ILE* 2.9 41.5 + - + +
212A MET* 4.2 8.1 - - + -
215A LEU* 4.1 23.6 - - + +
216A LEU* 3.8 30.5 - - + -
306A TYR* 3.6 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP* 2.9 35.6 + - - +
124A ASP* 3.5 16.2 - - - +
126A VAL* 1.3 75.1 - - - +
128A PHE* 1.3 57.6 + - - +
131A TYR* 2.9 32.1 + - - +
277A ASN* 4.2 4.0 + - - -
306A TYR* 3.4 52.1 + - + +
307A PHE* 3.4 5.8 - - + -
309A GLN* 3.1 34.1 - - - +
310A TYR* 3.8 12.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP 3.3 4.3 + - - +
125A HIS* 3.2 9.5 + - - +
126A VAL 3.2 0.4 - - - -
127A GLN* 1.3 78.6 - - - +
129A LEU* 1.3 64.3 + - + +
131A TYR* 3.5 7.4 + + - +
132A GLN* 3.1 65.4 + - + +
160A ASP 4.3 5.6 - - - -
161A CYS* 3.5 31.9 - - + -
162A GLU* 4.6 6.5 - - + -
310A TYR* 3.5 45.8 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.1 21.1 - - + -
115A ILE* 5.6 2.9 - - + -
121A LEU* 4.0 26.9 - - + -
125A HIS* 2.9 31.1 + - + +
126A VAL 4.1 1.6 - - - +
128A PHE* 1.3 77.8 - - + +
130A ILE* 1.3 63.5 + - + +
132A GLN* 3.3 9.3 + - - +
133A ILE* 3.1 27.1 + - - +
157A VAL* 4.3 11.2 - - + -
161A CYS* 3.5 37.5 - - + +
163A LEU* 3.8 15.4 - - + +
215A LEU* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 2.9 36.3 + - + +
129A LEU* 1.3 71.3 - - - +
131A TYR* 1.3 66.7 + - - +
133A ILE* 3.3 22.2 + - + +
134A LEU* 3.0 31.1 + - + +
208A VAL* 3.8 18.4 - - + -
211A ILE* 4.2 2.9 - - + -
212A MET* 3.8 36.3 - - + +
215A LEU* 3.8 19.5 - - + -
287A MET* 4.6 0.7 - - + -
306A TYR* 5.3 0.4 - - + -
307A PHE* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLN 2.9 21.8 + - - +
128A PHE* 3.6 10.5 - + - +
129A LEU 3.3 0.2 - - - -
130A ILE* 1.3 74.5 - - - +
132A GLN* 1.3 69.2 + - + +
134A LEU* 3.2 6.3 + - - +
135A ARG* 2.9 50.5 + - - +
302A LEU* 3.5 20.4 - - + -
307A PHE* 3.5 26.1 - - + -
310A TYR* 3.5 38.4 + + + -
311A HIS* 3.8 14.1 - - + -
312A ASP* 4.0 2.4 + - - +
315A ASP* 4.5 1.9 + - - +
316A GLU* 2.5 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN* 3.3 35.8 + - - +
128A PHE* 3.1 51.7 + - + +
129A LEU* 3.6 6.2 - - - +
131A TYR* 1.3 86.2 - - + +
133A ILE* 1.3 64.6 + - - +
135A ARG* 4.3 2.0 - - - -
136A GLY* 3.0 19.2 + - - -
161A CYS 2.8 23.2 + - - -
162A GLU* 3.4 9.7 - - - +
163A LEU* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.4 2.9 - - + -
129A LEU 3.1 17.4 + - - +
130A ILE* 3.3 28.9 + - + +
132A GLN* 1.3 75.2 - - - +
134A LEU* 1.3 58.3 + - - +
136A GLY* 3.3 1.4 + - - -
137A LEU* 2.8 29.8 + - + +
150A LEU* 4.1 14.8 - - + -
155A LEU* 3.5 32.3 - - + -
163A LEU* 3.7 25.8 - - + +
165A ILE* 3.7 6.0 - - + +
208A VAL* 3.8 28.9 - - + -
211A ILE* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 3.0 19.9 + - + +
131A TYR 3.7 3.6 - - - +
133A ILE* 1.3 77.6 - - - +
135A ARG* 1.3 56.1 + - - +
137A LEU* 3.7 2.4 - - + -
138A LYS* 2.8 30.0 + - - +
205A ILE* 3.8 28.9 - - + -
208A VAL* 4.2 13.7 - - + -
287A MET* 3.8 20.0 - - + -
298A ALA* 3.7 10.9 - - + +
301A ALA* 3.7 20.2 - - + -
302A LEU* 3.8 16.5 - - + +
307A PHE* 3.5 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.5 23.0 + - + +
80A GLU* 3.0 40.3 + - - +
81A ASN* 2.9 29.0 + - - +
131A TYR* 2.9 44.3 + - + +
132A GLN* 3.7 2.2 - - - +
133A ILE 3.3 0.2 - - - -
134A LEU* 1.3 76.3 - - - +
136A GLY* 1.3 63.2 + - - +
138A LYS* 3.5 3.8 + - - +
139A TYR 3.4 14.2 + - - -
302A LEU* 3.8 14.1 - - + +
315A ASP* 2.8 49.2 + - - -
316A GLU* 4.1 13.7 - - + +
317A PRO* 4.0 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.9 4.3 + - - -
81A ASN* 3.9 9.2 - - - +
82A VAL* 3.8 18.5 - - - +
132A GLN 3.0 13.2 + - - -
133A ILE 3.7 3.1 - - - -
135A ARG* 1.3 74.9 - - - +
137A LEU* 1.3 59.2 + - - +
139A TYR* 3.2 5.5 + - - +
140A ILE* 3.0 30.3 + - - +
165A ILE* 3.9 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 2.8 24.3 + - + +
134A LEU* 3.3 6.9 + - + +
136A GLY* 1.3 69.2 - - - +
138A LYS* 1.3 67.4 + - - +
140A ILE* 4.3 11.7 - - + -
141A HIS* 2.8 49.1 + - + +
147A HIS* 4.7 6.3 - - + -
150A LEU* 3.9 13.0 - - + -
165A ILE* 3.8 13.9 - - + +
204A ASP* 3.9 25.1 - - + +
205A ILE* 4.4 10.1 - - + -
208A VAL* 3.4 32.3 - - + -
298A ALA* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU 2.8 18.1 + - - +
135A ARG 3.6 6.5 - - - +
136A GLY 3.3 0.2 - - - -
137A LEU* 1.3 74.5 - - - +
139A TYR* 1.3 58.7 + - - +
141A HIS* 3.9 4.2 - - - +
142A SER* 3.0 28.8 + - - -
298A ALA* 3.7 11.8 - - + +
299A ALA* 4.4 22.6 - - + +
302A LEU* 3.8 23.5 - - + +
313A PRO* 4.9 6.5 + - - +
316A GLU* 2.8 39.2 + - + +
317A PRO 4.5 4.3 - - - +
318A VAL* 3.9 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS* 3.4 11.6 + - - -
77A MET* 3.7 28.8 - - + +
78A LYS* 2.9 40.4 + - - +
79A HIS* 3.5 42.4 - + + +
82A VAL* 4.2 5.8 - - + -
135A ARG 3.4 0.8 + - - -
136A GLY 3.2 7.6 + - - +
137A LEU 3.1 0.4 - - - -
138A LYS* 1.3 77.0 - - - +
140A ILE* 1.3 66.9 + - - +
142A SER* 2.6 24.2 + - - -
143A ALA 3.4 2.6 + - - -
317A PRO* 3.8 13.4 + - + +
318A VAL 3.6 9.6 - - - -
319A ALA* 3.3 46.8 - - + +
320A ASP 4.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A MET* 4.4 9.9 - - - -
82A VAL* 4.0 26.0 - - + -
136A GLY 3.0 20.3 + - - +
137A LEU* 3.2 11.9 + - + +
139A TYR* 1.3 76.5 - - - +
141A HIS* 1.3 62.1 + - + +
143A ALA* 3.0 23.7 + - - +
145A ILE* 3.3 51.6 + - + +
146A ILE 4.7 0.2 - - - +
147A HIS* 4.8 5.4 - - + +
165A ILE* 3.7 35.9 - - + -
168A PHE* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 2.8 42.3 + - + +
138A LYS* 3.9 3.8 - - - +
140A ILE* 1.3 75.7 - - + +
142A SER* 1.3 55.8 + - - +
143A ALA 3.1 0.2 - - - -
144A ASP* 2.9 14.2 + - - +
145A ILE 3.3 17.7 - - - -
201A GLN* 2.8 70.7 + - + +
204A ASP* 2.8 32.9 + - + +
205A ILE* 4.8 9.6 - - + -
298A ALA* 4.4 13.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LYS* 3.0 15.4 + - - -
139A TYR 2.6 20.4 + - - -
141A HIS* 1.3 76.2 - - - +
143A ALA* 1.3 56.4 + - - +
144A ASP* 3.3 5.7 + - - +
318A VAL* 3.6 24.4 - - - +
319A ALA* 2.8 28.6 + - - +
320A ASP 5.2 0.3 - - - +
321A PRO* 5.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS* 4.1 4.7 - - + -
77A MET* 4.5 2.0 - - + -
139A TYR 4.1 0.7 - - - +
140A ILE 3.0 12.3 + - - +
142A SER* 1.3 78.6 + - - +
144A ASP* 1.3 68.7 + - - +
145A ILE* 3.3 22.9 + - + +
319A ALA* 3.8 20.6 - - + -
320A ASP 4.1 6.1 - - - +
321A PRO* 5.5 1.1 - - - -
322A TYR* 3.8 29.3 + - + +
324A GLN* 4.0 3.3 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il