Contacts of the helix formed by residues 32 - 43 (chain B) in PDB entry 2HEI
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 GLY 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ALA 3.3 0.6 - - - -
31B VAL* 1.4 78.9 - - - +
33B LYS* 1.3 61.0 + - - +
34B SER 3.3 2.7 - - - -
35B SER* 3.3 1.2 + - - -
36B LEU* 2.8 38.3 + - - +
99B VAL* 4.8 0.2 - - - -
133B ASN* 3.6 10.8 - - - -
301B GDP 3.1 31.4 + - - -
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 3.7 18.2 - - + +
26B LEU 3.6 32.8 - - - +
27B GLY 2.9 16.9 + - - +
28B GLU 3.2 8.3 + - - -
31B VAL* 3.9 11.7 - - + +
32B GLY* 1.3 74.8 - - - +
34B SER* 1.3 61.8 + - - +
36B LEU* 3.2 4.4 + - - +
37B VAL* 3.1 26.7 + - - +
75B ASP* 3.5 10.8 - - - +
76B THR* 3.8 10.3 - - - +
77B ALA* 3.7 21.5 - - - +
80B GLU* 2.8 28.3 + - - -
99B VAL* 4.2 9.4 - - + +
301B GDP 2.8 25.4 + - - +
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Residues in contact with SER 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS* 1.3 72.4 - - - +
35B SER* 1.3 56.5 + - - +
37B VAL* 3.3 2.4 + - - +
38B LEU* 2.9 36.7 + - - +
50B GLU 5.0 0.9 - - - -
51B SER* 4.1 0.9 - - - -
52B THR 3.4 30.0 + - - -
53B ILE* 4.0 2.9 - - - -
75B ASP* 2.6 26.0 + - - -
77B ALA* 3.2 10.4 - - - +
301B GDP 2.6 30.8 + - - -
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLY 3.6 1.6 - - - -
33B LYS 3.3 0.2 - - - -
34B SER* 1.3 77.2 - - - +
36B LEU* 1.3 56.0 + - - +
38B LEU* 3.4 6.9 + - - +
39B ARG* 2.9 31.0 + - - +
44B GLN 4.8 0.7 - - - +
45B PHE* 3.8 12.7 - - - -
46B HIS 5.5 1.2 + - - -
164B ALA* 3.6 13.4 - - - +
301B GDP 2.7 60.8 + - - -
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.5 8.3 - - + -
32B GLY 2.8 19.9 + - - +
33B LYS 3.2 4.5 + - - +
35B SER* 1.3 77.4 - - - +
37B VAL* 1.3 63.0 + - - +
39B ARG* 3.4 3.6 + - - +
40B PHE* 3.0 24.6 + - - +
97B ILE* 5.5 2.0 - - + -
99B VAL* 3.8 38.1 - - + -
131B ALA* 4.5 7.0 - - + -
133B ASN* 3.5 25.8 - - - +
162B THR* 3.6 15.9 - - + +
164B ALA* 4.0 7.0 - - + +
170B VAL* 3.6 33.5 - - + +
173B LEU* 5.6 3.6 - - + -
174B PHE* 4.6 7.0 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.5 33.2 - - + -
33B LYS 3.1 15.4 + - - +
34B SER* 3.7 0.9 - - - +
36B LEU* 1.3 76.3 - - - +
38B LEU* 1.3 57.3 + - - +
40B PHE* 3.3 5.3 + - - +
41B VAL* 2.9 42.6 + - + +
53B ILE* 3.6 30.1 - - + -
58B LEU* 4.0 10.3 - - + -
73B ILE* 3.8 20.9 - - + -
75B ASP* 4.8 6.7 - - + -
174B PHE* 5.2 4.0 - - + -
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B SER 2.9 22.1 + - - +
35B SER* 4.0 5.8 - - - +
37B VAL* 1.3 75.7 - - - +
39B ARG* 1.3 58.5 + - - +
41B VAL* 4.7 0.2 - - - -
42B LYS* 2.8 49.4 + - + +
43B GLY 3.3 4.0 + - - -
44B GLN 3.8 7.6 - - - +
49B GLN* 3.4 28.9 - - + +
52B THR 4.0 17.0 - - - +
53B ILE* 4.1 15.5 - - + +
58B LEU* 3.8 24.9 - - + -
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER 2.9 18.8 + - - +
36B LEU* 3.8 4.9 - - - +
38B LEU* 1.3 77.2 - - - +
40B PHE* 1.3 58.8 + - - +
43B GLY* 2.9 51.3 + - - -
44B GLN* 3.4 14.9 + - - +
45B PHE* 3.4 15.6 - - + +
164B ALA* 2.9 23.4 + - - +
165B LYS 2.8 29.5 + - - -
166B THR 3.6 6.9 + - - -
167B ALA* 3.4 30.6 - - + +
170B VAL* 4.1 17.5 - - + -
171B ASN* 4.8 3.1 - - - +
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Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU 3.0 18.1 + - - +
37B VAL 3.7 2.2 - - - +
39B ARG* 1.3 78.1 - - - +
41B VAL* 1.3 59.9 + - - +
43B GLY* 4.3 1.4 + - - -
60B GLN* 3.1 47.8 + - + -
61B SER 4.1 3.1 - - - -
62B VAL* 3.8 20.6 - - + -
71B PHE* 4.2 9.2 - + - -
73B ILE* 3.6 25.4 - - + -
170B VAL* 4.1 3.5 - - + +
171B ASN* 3.5 33.5 - - + +
174B PHE* 3.6 57.7 - + + -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 2.9 27.2 + - + +
40B PHE* 1.3 76.2 - - - +
42B LYS* 1.3 80.6 + - + +
58B LEU* 3.8 38.1 - - + -
59B THR 3.7 16.6 - - - +
60B GLN* 3.1 36.0 + - + +
73B ILE* 4.1 13.0 - - + -
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 2.8 36.9 + - + +
41B VAL* 1.3 91.8 - - + +
43B GLY* 1.3 58.6 + - - +
44B GLN* 3.3 19.3 + - + +
58B LEU* 4.5 19.0 - - - +
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU 3.3 0.4 + - - -
39B ARG* 2.9 44.0 + - - -
40B PHE 4.3 2.4 + - - -
41B VAL 3.6 1.4 - - - -
42B LYS* 1.3 76.3 - - - +
44B GLN* 1.3 62.0 + - - +
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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