Contacts of the helix formed by residues 117 - 138 (chain A) in PDB entry 5TQW
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 LYS 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 5.1 1.6 + - - -
116A LEU* 1.3 74.6 - - - +
118A GLU* 1.3 67.7 + - + +
119A SER* 3.8 19.7 - - - +
120A GLN* 3.3 42.9 + - + +
121A ILE* 3.3 23.4 + - - +
263A SER* 3.9 6.5 - - - +
439A GLU* 4.7 13.6 + - - -
443A ARG* 4.4 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 1.3 74.5 - - + +
119A SER* 1.3 59.9 + - - +
121A ILE* 3.0 15.8 + - - +
122A LEU* 2.9 38.8 + - + +
263A SER* 2.9 32.0 + - - +
264A LEU* 3.3 31.1 - - + +
265A CYS* 3.2 20.0 + - - +
268A ILE* 3.5 31.4 - - - +
269A VAL* 5.2 0.2 - - - +
314A HIS* 5.4 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 3.5 18.4 - - - +
118A GLU* 1.3 78.0 - - - +
120A GLN* 1.3 61.8 + - - +
122A LEU* 3.2 19.7 + - - +
123A SER* 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 5.8 3.3 - - - +
116A LEU* 4.8 8.5 - - + +
117A LYS* 3.3 55.5 + - + +
118A GLU 3.2 0.6 - - - -
119A SER* 1.3 79.2 + - - +
121A ILE* 1.3 58.7 + - + +
123A SER* 2.4 25.0 + - - -
124A LEU* 2.9 12.5 + - - +
161A HIS* 4.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.7 31.0 - - + +
117A LYS 3.3 17.0 + - - +
118A GLU* 3.0 11.1 + - - +
120A GLN* 1.3 74.6 - - - +
122A LEU* 1.3 59.9 + - + +
124A LEU* 3.2 14.2 + - + +
125A LEU* 2.9 28.2 + - + +
211A VAL* 4.4 13.7 - - + -
214A CYS* 3.4 37.9 - - + +
215A ILE* 3.9 27.8 - - + -
264A LEU* 5.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 2.9 29.3 + - + +
119A SER* 3.3 22.9 - - - +
120A GLN 3.2 0.4 - - - -
121A ILE* 1.3 77.8 - - + +
123A SER* 1.3 60.2 + - - +
125A LEU* 3.3 10.7 + - + +
126A SER* 2.9 28.3 + - - -
268A ILE* 4.6 23.8 - - + -
272A MET* 5.6 9.6 - - + -
307A ILE* 3.7 30.7 - - + +
308A LEU* 4.9 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER 2.9 11.8 + - - -
120A GLN* 2.4 29.7 + - - +
122A LEU* 1.3 71.3 - - - +
124A LEU* 1.3 59.5 + - - +
126A SER* 3.4 7.6 + - - -
127A ASP* 2.9 40.8 + - - +
159A ILE 5.2 3.6 + - - -
161A HIS* 4.2 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.0 19.5 - - + -
116A LEU* 5.5 2.5 - - + -
120A GLN 2.9 14.5 + - - +
121A ILE* 3.2 18.4 - - + +
123A SER* 1.3 77.6 + - - +
125A LEU* 1.3 58.6 + - - +
127A ASP 3.3 0.2 + - - -
128A ILE* 2.8 47.3 + - + +
150A ILE* 4.6 0.4 - - + -
161A HIS* 3.4 39.5 - - + +
207A PHE* 6.4 0.4 - - + -
210A MET* 5.5 8.3 - - + -
211A VAL* 5.3 9.9 - - + -
214A CYS* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 2.9 16.8 + - + +
122A LEU* 3.3 10.9 + - + +
124A LEU* 1.3 75.6 - - - +
126A SER* 1.3 62.0 + - - +
129A GLY* 2.9 27.2 + - - -
207A PHE* 4.1 10.3 - - + -
211A VAL* 4.2 15.7 - - + -
272A MET* 3.8 18.6 - - + -
275A TRP* 3.6 34.3 - - + -
304A MET* 3.7 42.0 - - + +
307A ILE* 5.2 12.1 - - + -
308A LEU* 5.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU 2.9 16.6 + - - -
123A SER* 3.6 8.5 - - - -
125A LEU* 1.3 79.1 - - - +
127A ASP* 1.3 60.8 + - - +
130A SER* 2.9 31.2 + - - -
133A ARG* 5.9 0.3 + - - -
308A LEU* 3.7 38.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER* 2.9 19.4 + - - +
124A LEU 3.8 2.5 - - - +
126A SER* 1.3 78.8 + - - +
128A ILE* 1.3 60.6 + - - +
130A SER* 2.6 22.5 + - - -
131A GLY* 2.9 11.3 + - - -
159A ILE 3.7 8.1 - - - +
160A ILE* 3.9 16.0 - - - +
161A HIS* 3.2 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 2.8 38.6 + - + +
127A ASP* 1.3 69.7 - - - +
129A GLY* 1.3 59.6 + - - +
131A GLY* 3.3 2.5 + - - +
132A ILE* 2.9 31.8 + - + +
145A LEU* 4.7 2.5 - - + -
150A ILE* 3.7 22.2 - - + -
161A HIS* 3.3 34.3 - - + +
163A ILE* 3.8 25.4 - - + -
207A PHE* 3.5 23.3 - - + -
210A MET* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU 2.9 23.7 + - - -
128A ILE* 1.3 78.0 - - - +
130A SER* 1.3 56.5 + - - +
132A ILE* 3.2 8.6 - - - +
133A ARG* 2.9 38.1 + - - +
207A PHE* 3.8 4.5 - - - -
301A PHE* 4.3 0.3 - - - -
304A MET* 3.7 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER 2.9 16.7 + - - -
127A ASP* 2.6 23.2 + - - -
129A GLY* 1.3 72.4 - - - +
131A GLY* 1.3 59.8 + - - +
133A ARG* 3.5 18.1 - - - +
134A TYR* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASP 2.9 14.9 + - - -
128A ILE* 3.3 4.7 + - - -
129A GLY 3.2 0.4 - - - -
130A SER* 1.3 78.5 + - - +
132A ILE* 1.3 58.6 + - - +
134A TYR* 3.1 9.8 + - - +
135A LEU* 2.9 34.3 + - - +
163A ILE* 4.8 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 2.9 19.6 + - + +
129A GLY* 3.2 13.9 - - - +
131A GLY* 1.3 74.0 - - - +
133A ARG* 1.3 59.8 + - - +
135A LEU* 4.2 9.4 - - + +
136A HIS* 3.0 44.4 + - + +
142A HIS* 5.9 1.6 - - + -
145A LEU* 3.8 32.5 - - + -
163A ILE* 4.4 7.2 - - + -
203A ASP* 4.8 5.8 - - + +
204A TYR* 5.2 8.3 - - + -
207A PHE* 3.6 41.5 - - + -
279A MET* 6.0 0.4 - - + -
301A PHE* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER 5.9 0.4 + - - -
129A GLY 2.9 20.4 + - - +
130A SER* 3.5 17.4 - - - +
132A ILE* 1.3 77.4 - - - +
134A TYR* 1.3 55.7 + - - +
136A HIS* 3.8 1.0 - - - +
137A GLU* 3.0 39.4 + - - +
297A GLN* 4.1 10.1 - - + +
301A PHE* 2.5 78.6 + - + +
304A MET* 3.4 22.3 - - - +
305A ASP* 2.7 23.3 + - - -
308A LEU* 4.8 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS 4.9 11.3 + - - -
130A SER 2.9 15.6 + - - +
131A GLY* 3.1 12.1 + - - +
133A ARG* 1.3 75.7 - - - +
135A LEU* 1.3 70.5 + - + +
137A GLU* 3.2 29.3 - - - +
138A ASN* 2.5 59.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLY 2.9 19.7 + - - +
132A ILE* 3.5 7.6 + - + +
133A ARG 3.3 0.2 - - - -
134A TYR* 1.3 91.9 - - + +
136A HIS* 1.3 62.2 + - + +
137A GLU 3.2 1.3 - - - -
138A ASN* 2.8 13.5 + - - +
140A ILE* 2.7 72.5 + - + +
142A HIS* 4.5 19.5 - - + +
163A ILE* 4.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.0 27.9 + - + +
133A ARG* 4.2 3.8 - - - +
135A LEU* 1.3 75.1 - - + +
137A GLU* 1.3 64.9 + - - +
139A LYS* 3.9 7.4 + - - +
140A ILE 3.1 23.1 - - - +
141A ILE* 4.3 5.3 - - + -
200A ALA* 3.5 27.6 - - + +
203A ASP* 3.6 26.9 + - + +
204A TYR* 3.3 41.2 + + - +
301A PHE* 4.5 8.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 3.0 27.9 + - + +
134A TYR* 3.2 36.7 - - - +
136A HIS* 1.3 78.3 - - - +
138A ASN* 1.3 62.5 + - - +
139A LYS* 3.2 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 4.8 15.4 + - - -
134A TYR* 2.5 59.6 + - - -
135A LEU* 2.8 10.9 + - - +
137A GLU* 1.3 80.4 - - - +
139A LYS* 1.3 71.0 + - - +
140A ILE* 3.2 23.8 - - + +
----------------------------------------------------------
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