Contacts of the helix formed by residues 127 - 141 (chain A) in PDB entry 1ULH
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 LEU 127 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A MET* 6.2 2.7 - - + -
123A HIS 4.4 0.2 - - - +
124A VAL* 3.3 27.6 - - + +
125A GLY 2.8 0.8 + - - -
126A HIS* 1.3 78.2 - - - +
128A ILE* 1.3 58.3 + - - +
129A PRO 3.4 0.4 - - - -
130A PHE* 3.3 5.0 + - + +
131A ILE* 2.7 53.5 + - + +
178A CYS* 3.7 29.2 - - - -
314A LEU* 3.6 44.9 - - + -
359A PHE* 4.6 2.7 - - + -
394A LEU* 4.5 17.9 - - + -
398A HIS* 4.5 8.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
84A PHE* 3.2 46.2 - - + -
89A ILE* 4.1 11.4 - - + -
90A PHE* 4.0 12.7 - - + -
125A GLY 2.9 14.0 + - - +
127A LEU* 1.3 78.8 - - - +
129A PRO* 1.4 71.7 - - + +
131A ILE* 4.7 0.2 - - - -
132A PHE* 3.4 9.0 + - - +
290A SER* 5.0 6.1 - - - +
291A THR 5.7 1.6 - - - +
293A PHE* 3.9 19.3 - - + -
358A PHE* 3.4 26.7 - - + -
359A PHE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 4.3 14.8 - - + -
113A THR* 4.8 9.4 - - - +
125A GLY 4.1 3.8 - - - +
126A HIS* 4.1 13.7 - - - +
127A LEU 4.0 0.4 - - - -
128A ILE* 1.4 95.5 - - + +
130A PHE* 1.3 58.7 + - + +
132A PHE* 3.3 3.5 + - - +
133A THR* 2.7 42.3 + - - +
261A PRO* 4.6 16.4 - - - +
262A CYS* 5.3 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A THR* 3.9 28.0 - - + -
114A GLY 3.8 18.4 - - - -
115A ARG* 4.1 10.1 - - + -
122A MET* 4.0 21.8 - - + -
126A HIS 3.1 26.2 - - - -
127A LEU* 3.3 6.4 + - + +
129A PRO* 1.3 79.6 - - + +
131A ILE* 1.3 61.0 + - - +
133A THR* 4.2 2.0 - - - -
134A LYS* 2.8 32.8 + - - +
146A ILE* 4.1 14.1 - - + -
175A ILE* 3.9 22.7 - - + -
178A CYS* 4.1 20.6 - - - -
180A PHE* 3.5 31.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A HIS* 3.8 24.2 - - + +
83A HIS* 5.6 2.7 - - + -
84A PHE* 4.4 10.3 - - + -
127A LEU* 2.7 41.1 + - + +
128A ILE 4.1 4.3 - - - +
130A PHE* 1.3 71.7 - - - +
132A PHE* 1.3 57.5 + - - +
134A LYS* 3.4 9.0 + - - +
135A TRP* 3.1 24.9 + - - +
178A CYS* 5.9 4.5 - - + -
359A PHE* 3.6 34.8 - - + -
394A LEU* 5.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A HIS* 4.0 18.8 - + + -
84A PHE* 3.6 32.5 - + + -
85A LEU* 3.7 36.8 - - + -
90A PHE* 3.4 45.8 - + + -
128A ILE 3.4 15.5 + - - +
129A PRO 3.3 3.1 + - - +
130A PHE 3.2 0.2 - - - -
131A ILE* 1.3 78.4 - - - +
133A THR* 1.3 60.6 + - - +
135A TRP* 3.2 13.3 + + - +
136A LEU* 2.9 42.3 + - + +
261A PRO* 4.5 3.1 - - + -
288A LEU* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.8 16.3 - - + +
113A THR* 4.3 13.9 - - + +
129A PRO* 2.7 30.6 + - - +
130A PHE* 3.8 6.0 - - - -
132A PHE* 1.3 72.4 - - - +
134A LYS* 1.3 58.8 + - - +
136A LEU* 3.1 12.5 + - - +
137A GLN* 2.8 28.2 + - - +
144A LEU* 3.4 40.4 - - + -
180A PHE* 4.2 5.2 - - - -
261A PRO* 3.8 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE 2.8 18.2 + - - +
131A ILE* 3.4 9.2 - - + +
133A THR* 1.3 77.5 - - - +
135A TRP* 1.3 60.3 + - - +
137A GLN* 3.2 5.5 + - - +
138A ASP* 2.7 59.0 + - - +
178A CYS* 3.1 29.2 - - + +
179A GLY* 3.3 25.0 + - - -
180A PHE* 3.5 29.2 - - + +
181A ASP 5.4 0.8 - - - +
401A ARG* 5.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 4.5 19.7 - - + -
77A THR* 4.5 6.7 - - + -
79A GLN* 4.6 3.9 - - + +
80A ARG 3.7 14.0 + - - -
81A PRO* 4.1 8.3 - - + -
82A HIS* 3.6 59.3 - + + +
85A LEU* 4.2 15.5 - - + -
131A ILE 3.1 13.6 + - - +
132A PHE* 3.4 17.0 - + - +
134A LYS* 1.3 76.5 - - - +
136A LEU* 1.3 84.6 + - + +
138A ASP* 2.9 19.3 + - + +
139A VAL* 2.9 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A MET* 5.4 1.3 - - + -
111A LEU* 3.7 19.5 - - + -
132A PHE* 2.9 36.6 + - + +
133A THR* 3.3 7.4 - - - +
135A TRP* 1.3 85.0 - - + +
137A GLN* 1.3 63.2 + - - +
139A VAL* 4.0 4.9 - - - -
140A PHE* 3.1 58.0 + - + +
142A VAL* 4.5 0.5 - - - +
259A LEU* 4.1 15.5 - - + -
261A PRO* 3.7 31.0 - - + -
288A LEU* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.6 12.9 - - + +
133A THR 2.8 13.5 + - - +
134A LYS* 3.4 9.7 - - - +
136A LEU* 1.3 77.6 - - - +
138A ASP* 1.3 57.3 + - - +
141A ASN* 2.8 29.1 + - - -
142A VAL 3.4 15.7 + - - +
144A LEU* 3.4 17.4 - - + +
180A PHE* 3.5 18.2 - - - -
181A ASP 3.7 9.6 + - - -
184A LYS* 2.7 52.2 + - + +
185A THR* 2.9 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 2.7 46.6 + - - +
135A TRP* 2.9 10.5 + - + +
137A GLN* 1.3 80.4 - - - +
139A VAL* 1.3 68.4 + - + +
141A ASN* 3.8 7.8 + - - +
181A ASP* 5.1 2.6 + - - +
184A LYS* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA 5.5 0.2 - - - +
77A THR* 3.5 29.9 - - + +
79A GLN* 3.6 25.9 - - + +
103A TYR* 3.7 6.1 + - - -
135A TRP* 2.9 64.7 + - + +
136A LEU* 3.7 0.9 - - - +
138A ASP* 1.3 77.7 - - + +
140A PHE* 1.3 87.7 + - + +
141A ASN* 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.6 28.0 - - + -
76A ALA* 5.1 1.3 - - + -
77A THR* 3.7 9.4 - - - -
96A MET* 4.4 14.8 - - + -
99A VAL* 6.1 0.2 - - + -
100A LEU* 4.2 15.7 - - + -
103A TYR* 2.6 58.7 + + + -
109A PHE* 3.5 37.7 - + + -
135A TRP* 4.9 0.7 - + - -
136A LEU* 3.1 52.4 + - + +
139A VAL* 1.3 89.4 - - + +
141A ASN* 1.3 71.9 + - - +
142A VAL* 3.8 4.8 - - + +
422A ASP* 3.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 5.0 0.2 - - - +
137A GLN 2.8 16.9 + - - -
138A ASP 3.8 6.7 + - - +
139A VAL 3.5 2.1 - - - +
140A PHE* 1.3 80.4 - - - +
142A VAL* 1.3 56.0 + - - +
184A LYS* 3.2 31.6 - - - +
420A SER 4.4 8.1 + - - -
421A PHE 4.1 1.0 - - - -
422A ASP* 2.7 49.9 + - - +
----------------------------------------------------------
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