Contacts of the helix formed by residues 32 - 45 (chain S) in PDB entry 1H2I
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 32 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203R ALA 4.4 2.1 + - - -
207R SER* 4.0 33.4 - - - +
30S GLN 4.7 4.9 - - - +
31S TYR* 1.3 74.9 - - - +
33S ALA* 1.3 66.7 + - - +
34S GLU* 3.7 8.0 + - - +
35S GLU* 3.1 24.9 + - - +
36S TYR* 2.9 21.0 + - - +
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Residues in contact with ALA 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205Q TYR* 2.9 36.0 - - + +
208Q CYS* 3.5 44.6 + - + +
209Q ARG* 5.4 3.8 - - + -
31S TYR 3.8 1.4 + - - -
32S THR* 1.3 72.6 - - - +
34S GLU* 1.3 57.2 + - - +
36S TYR* 3.7 1.7 - - - +
37S GLN 2.9 25.1 + - - -
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Residues in contact with GLU 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205Q TYR* 3.5 12.1 + - - +
199R SER 5.2 0.7 - - - +
202R GLU* 4.7 9.0 - - - +
203R ALA* 3.5 30.9 + - + +
206R ASN* 4.1 23.2 + - - +
32S THR* 3.1 7.2 - - - +
33S ALA* 1.3 79.0 - - - +
35S GLU* 1.3 63.5 + - - +
37S GLN* 3.9 2.7 + - - +
38S ALA* 3.1 19.6 + - - +
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Residues in contact with GLU 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R TYR* 4.4 0.2 - - - -
200R VAL* 4.9 2.0 - - + +
203R ALA* 3.3 20.5 - - + +
204R ARG* 2.7 44.3 + - - +
207R SER* 3.8 16.3 - - - -
31S TYR* 3.6 24.8 - - + -
32S THR* 3.1 20.4 + - - +
34S GLU* 1.3 73.5 - - - +
36S TYR* 1.3 66.7 + - - +
38S ALA* 3.2 1.4 + - - +
39S ILE* 2.9 35.8 + - + +
79S PHE 4.5 0.2 - - - +
116S LYS* 3.2 22.6 + - - -
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Residues in contact with TYR 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201Q GLU* 3.7 13.4 + - - -
204Q ARG* 2.8 40.3 + - + -
205Q TYR* 4.3 15.3 - + - -
208Q CYS* 4.6 14.1 - - + -
80R GLY* 3.8 2.7 - - - -
81R TYR* 3.3 26.3 + + - -
82R ASN* 3.5 30.3 - - - -
31S TYR* 4.1 11.5 - - + +
32S THR 2.9 17.1 + - - +
33S ALA* 3.7 7.4 - - - +
35S GLU* 1.3 77.5 - - - +
37S GLN* 1.3 66.9 + - + +
40S GLN* 2.9 64.1 + - + +
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Residues in contact with GLN 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201Q GLU* 5.1 8.7 - - - +
205Q TYR* 3.1 56.5 + - + +
33S ALA 2.9 8.4 + - - +
34S GLU* 3.9 2.6 + - - +
36S TYR* 1.3 85.6 - - + +
38S ALA* 1.3 64.3 + - - +
40S GLN* 3.5 2.8 + - - +
41S LYS* 2.9 61.2 + - - +
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Residues in contact with ALA 38 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199R SER* 4.2 14.4 + - - +
200R VAL* 3.6 33.6 - - + +
203R ALA* 4.3 3.1 - - + -
34S GLU 3.1 17.0 + - - +
35S GLU 3.2 3.1 + - - +
37S GLN* 1.3 81.0 - - - +
39S ILE* 1.3 58.5 + - - +
41S LYS* 3.5 6.9 + - - +
42S ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 39 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81R TYR* 3.4 37.9 - - + +
200R VAL* 3.9 16.8 - - + -
204R ARG* 4.1 0.9 - - - +
31S TYR* 3.9 10.3 - - + -
35S GLU* 2.9 39.4 + - + +
38S ALA* 1.3 72.8 - - - +
40S GLN* 1.3 65.7 + - - +
41S LYS 3.1 1.6 - - - -
42S ALA* 4.3 2.0 - - - -
43S LEU* 2.8 43.7 + - + +
78S MET* 3.7 27.8 - - - +
79S PHE* 4.3 13.7 - - + -
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Residues in contact with GLN 40 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201Q GLU* 4.3 14.5 - - - +
204Q ARG* 4.5 0.3 + - - -
76R ASN* 3.0 27.3 + - - +
77R GLU* 4.1 13.0 + - - +
80R GLY* 3.4 6.1 - - - -
81R TYR* 3.7 25.8 - - + +
36S TYR* 2.9 52.1 + - + +
37S GLN* 3.5 5.8 + - - +
39S ILE* 1.3 76.8 - - - +
41S LYS* 1.3 65.6 + - + +
43S LEU* 3.5 9.7 + - - +
44S ARG* 3.6 27.9 + - - +
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Residues in contact with LYS 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201Q GLU* 5.7 2.2 - - - +
37S GLN* 2.9 50.0 + - + +
38S ALA* 3.7 8.3 - - - +
39S ILE 3.1 0.6 - - - -
40S GLN* 1.3 77.0 - - + +
42S ALA* 1.3 68.5 + - - +
44S ARG* 2.9 47.0 + - - +
45S GLN* 4.0 4.9 + - - +
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Residues in contact with ALA 42 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197R GLU* 3.5 27.1 - - - +
199R SER* 5.7 0.7 - - - +
200R VAL* 4.1 6.1 - - + -
38S ALA 2.9 19.0 + - - +
39S ILE 3.8 1.1 - - - +
41S LYS* 1.3 78.0 - - - +
43S LEU* 1.3 61.8 + - - +
44S ARG 3.2 0.9 + - - -
45S GLN* 3.3 27.9 + - - +
78S MET* 3.8 24.0 - - - +
161S ALA* 3.4 9.5 - - - +
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Residues in contact with LEU 43 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R TYR* 3.4 29.4 - - + -
39S ILE* 2.8 39.3 + - + +
40S GLN* 3.8 7.2 - - - +
41S LYS 3.0 0.4 + - - -
42S ALA* 1.3 71.0 - - - +
44S ARG* 1.3 57.4 + - + +
45S GLN 3.3 0.2 - - - -
78S MET* 3.8 15.3 - - + -
79S PHE* 4.6 2.5 - - + -
158S PHE* 3.3 37.9 - - + +
159S GLY* 4.5 2.0 - - - +
160S ASN 3.1 11.8 + - - -
161S ALA* 2.9 28.6 + - + -
162S LEU* 3.7 30.3 - - + -
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Residues in contact with ARG 44 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196Q LEU* 3.0 20.5 - - - +
201Q GLU* 4.4 18.6 + - - +
77R GLU* 2.5 51.7 + - - +
40S GLN* 3.6 23.6 + - - +
41S LYS* 2.9 42.2 + - - +
43S LEU* 1.3 77.8 - - - +
45S GLN* 1.3 64.1 + - - +
46S ARG* 3.5 3.6 + - - +
160S ASN* 3.0 23.7 + - - +
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Residues in contact with GLN 45 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190R LYS 4.9 10.8 - - - +
192R LYS* 3.2 32.8 - - + +
197R GLU* 3.1 32.7 + - - +
41S LYS 4.4 3.6 - - - +
42S ALA* 3.3 20.1 + - - +
43S LEU 3.3 0.8 - - - -
44S ARG* 1.3 76.9 - - - +
46S ARG* 1.3 65.4 + - - +
160S ASN* 3.1 1.7 - - - +
161S ALA* 2.8 33.7 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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