Contacts of the helix formed by residues 37 - 45 (chain B) in PDB entry 4X4W
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 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ALA* 1.3 74.0 - - - +
38B GLY* 1.3 62.6 - - - -
40B VAL* 3.1 14.9 + - - +
41B ARG* 3.3 9.5 + - - +
53B ASP* 4.5 2.7 - - - -
125B ARG* 3.8 13.8 - - - +
129B ILE 4.6 0.5 - - - +
130B ASN* 3.5 31.1 + - - +
132B MET 3.2 12.4 + - - +
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Residues in contact with GLY 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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36B ALA 3.5 1.0 + - - -
37B GLY* 1.3 69.4 - - - -
39B ALA* 1.3 59.7 + - - +
41B ARG* 3.2 33.4 + - - +
42B ASP* 2.9 34.7 + - - -
53B ASP* 5.5 2.4 + - - +
130B ASN* 4.4 2.9 + - - +
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Residues in contact with ALA 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 ILE* 3.7 23.1 - - + -
36B ALA 3.7 5.5 + - - +
37B GLY 3.2 0.8 - - - -
38B GLY* 1.3 75.2 - - - +
40B VAL* 1.3 61.9 + - - +
42B ASP* 3.4 2.5 + - - +
43B LEU* 3.1 28.9 + - - +
49B PRO* 3.7 27.9 - - + +
52B ILE* 3.8 24.2 - - + -
53B ASP* 4.6 1.5 - - - +
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Residues in contact with VAL 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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35B ILE* 3.4 39.9 - - + +
36B ALA 3.8 3.1 - - - -
37B GLY 3.1 7.5 + - - +
39B ALA* 1.3 75.3 - - - +
41B ARG* 1.3 66.8 + - - +
43B LEU* 3.4 7.6 + - - +
44B LEU* 2.9 29.7 + - + +
129B ILE 5.7 0.4 - - - +
132B MET* 3.6 27.6 - - + +
133B PHE 4.5 0.4 - - - -
134B LEU* 3.8 15.5 - - + +
140B LEU* 3.8 30.1 - - + -
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Residues in contact with ARG 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 GLY 3.3 3.6 + - - +
38B GLY* 3.2 30.1 + - - +
40B VAL* 1.3 79.6 - - - +
42B ASP* 1.3 87.9 + - - +
44B LEU* 3.3 8.2 + - - +
45B ASN* 3.0 39.6 + - - +
129B ILE* 3.5 43.9 + - + +
130B ASN* 2.7 34.1 + - - +
150B LEU* 4.1 8.4 - - + +
177B ARG* 4.7 4.9 - - - +
178B PHE* 3.2 36.3 - - - -
181B ARG* 3.8 16.9 - - - +
182B ILE* 4.5 6.1 - - - -
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Residues in contact with ASP 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 GLY 2.9 20.0 + - - +
39B ALA 3.7 4.5 - - - +
40B VAL 3.2 0.2 - - - -
41B ARG* 1.3 90.2 + - - +
43B LEU* 1.3 62.7 + - - +
45B ASN* 3.1 10.2 + - - +
46B GLY 3.0 6.2 + - - -
47B VAL* 2.9 38.6 + - + +
48B LYS 5.5 0.2 - - - -
49B PRO* 4.0 21.1 - - + +
50B GLN 5.0 0.9 + - - -
181B ARG* 2.7 34.3 + - - -
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Residues in contact with LEU 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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6B LEU* 4.2 21.0 - - + +
8B SER* 4.9 4.9 + - - +
10B GLU* 3.9 7.7 - - + +
11B PHE* 3.7 44.4 - - + +
14B LEU* 4.1 13.0 - - + -
35B ILE* 4.3 7.6 - - + -
39B ALA 3.1 20.0 + - - +
40B VAL* 3.7 5.2 - - + +
42B ASP* 1.3 79.7 - - - +
44B LEU* 1.3 61.9 + - + +
46B GLY* 3.1 13.6 + - - +
47B VAL 3.6 6.1 - - - +
49B PRO* 3.6 23.8 - - + -
134B LEU* 3.7 26.2 - - + -
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Residues in contact with LEU 44 (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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6B LEU* 4.9 19.5 - - + -
40B VAL* 2.9 30.9 + - + +
41B ARG* 3.7 0.4 - - - +
43B LEU* 1.3 76.4 - - + +
45B ASN* 1.3 57.4 + - - +
46B GLY 3.4 1.4 + - - -
132B MET* 3.6 37.5 - - + -
134B LEU* 5.8 2.5 - - + -
140B LEU* 4.1 15.3 - - + -
147B TYR* 4.1 32.0 - - + -
150B LEU* 3.4 25.6 - - + +
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Residues in contact with ASN 45 (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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41B ARG* 3.0 24.7 + - - +
42B ASP* 3.1 14.0 + - - +
44B LEU* 1.3 75.6 - - - +
46B GLY* 1.3 58.9 + - - +
47B VAL* 3.5 10.3 + - + +
150B LEU* 3.5 28.8 - - - +
181B ARG* 5.4 7.8 + - - +
182B ILE* 4.0 17.0 + - - +
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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