Contacts of the helix formed by residues 34 - 43 (chain B) in PDB entry 1WG8
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 ALA 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B LEU* 2.9 37.1 + - + +
32B GLY 3.2 1.2 - - - -
33B GLY* 1.3 82.1 - - - +
35B GLY* 1.3 58.6 + - - +
36B HIS 3.5 2.5 - - - -
37B ALA* 3.7 8.5 - - + +
38B ARG* 2.9 33.5 + - + +
60B ALA* 4.8 5.8 - - + -
63B LEU* 4.3 18.2 - - + -
65B LEU* 4.5 9.4 - - + -
68B LEU* 4.9 1.3 - - + -
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Residues in contact with GLY 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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8B PRO* 4.2 15.7 - - - +
11B TYR* 3.4 15.1 - - - -
33B GLY 3.3 2.5 - - - -
34B ALA* 1.3 78.7 - - - +
36B HIS* 1.3 62.9 + - - +
38B ARG* 3.5 15.9 + - - +
39B GLY 3.6 2.1 + - - -
3141B SAM 3.0 17.5 + - - -
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Residues in contact with HIS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 3.6 22.3 - - + +
9B VAL 3.0 25.4 + - - -
11B TYR* 4.1 22.0 - + - -
14B ALA* 4.3 8.9 - - + +
15B LEU* 3.8 6.7 - - + +
28B ASP* 4.0 6.5 - - - +
34B ALA 3.5 0.2 - - - -
35B GLY* 1.3 73.7 - - - +
37B ALA* 1.3 62.6 + - - +
39B GLY* 3.1 11.8 + - - -
40B ILE* 3.2 17.7 + - - +
94B LEU* 3.4 32.1 - - + +
96B ASP* 3.4 30.7 - - + +
232B ILE* 4.3 5.9 - - + +
3141B SAM 2.8 33.9 + - - +
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASP* 3.5 18.4 + - - +
31B LEU* 4.0 17.3 - - + -
34B ALA* 3.3 11.2 + - + +
35B GLY 3.2 0.4 - - - -
36B HIS* 1.3 76.4 - - - +
38B ARG* 1.3 67.6 + - - +
40B ILE* 3.0 12.2 + - - +
41B LEU* 3.0 29.4 + - + +
47B VAL* 4.2 18.6 - - + -
65B LEU* 5.8 0.2 - - + -
68B LEU* 4.8 7.6 - - + -
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 5.2 1.8 - - - +
33B GLY 5.1 4.9 + - - -
34B ALA* 2.9 22.1 + - - +
35B GLY* 3.7 9.8 - - - +
37B ALA* 1.3 74.8 - - - +
39B GLY* 1.3 58.4 + - - +
41B LEU* 3.3 11.0 + - - +
42B GLU* 2.9 43.1 + - + +
63B LEU* 3.8 32.5 - - - +
65B LEU* 3.7 31.9 - - + +
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Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 2.9 31.0 + - - -
15B LEU* 3.8 8.9 - - - +
35B GLY 3.6 2.0 + - - -
36B HIS 3.1 8.3 + - - -
37B ALA 3.1 0.8 - - - -
38B ARG* 1.3 80.0 - - - +
40B ILE* 1.3 61.1 + - - +
42B GLU* 3.5 6.8 + - - +
43B ARG* 3.2 28.6 + - - +
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Residues in contact with ILE 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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15B LEU* 3.8 15.0 - - + -
18B LEU* 3.5 26.2 - - + -
20B VAL* 3.9 9.3 - - + +
26B TYR* 3.7 37.2 - - + -
27B VAL 5.4 1.1 - - - +
28B ASP* 5.0 6.7 - - + -
36B HIS 3.2 14.8 + - - +
37B ALA* 3.0 10.8 + - - +
39B GLY* 1.3 72.4 - - - +
41B LEU* 1.3 67.4 + - - +
43B ARG* 3.1 14.2 + - - +
44B GLY 3.5 0.2 + - - -
45B GLY* 3.0 19.8 + - - -
47B VAL* 3.5 28.3 - - + -
94B LEU* 4.8 10.3 - - + -
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Residues in contact with LEU 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 ALA* 3.0 21.3 + - + +
38B ARG* 3.5 7.6 - - - +
40B ILE* 1.3 76.1 - - - +
42B GLU* 1.3 53.5 + - + +
44B GLY* 2.6 28.6 + - - -
45B GLY 3.1 21.2 + - - +
47B VAL* 3.6 14.8 - - + -
65B LEU* 3.9 28.7 - - + -
66B PRO* 3.3 28.7 - - + +
67B GLY* 3.6 19.3 - - - +
68B LEU* 4.2 10.1 - - + -
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 4.9 9.1 + - - -
38B ARG* 2.9 36.8 + - + +
39B GLY* 3.6 7.0 - - - +
40B ILE 3.2 0.2 - - - -
41B LEU* 1.3 76.1 - - + +
43B ARG* 1.3 60.5 + - + +
44B GLY* 3.0 5.0 + - - -
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Residues in contact with ARG 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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12B GLN* 2.8 39.2 + - - +
15B LEU* 3.6 38.4 + - - +
16B ASP* 3.2 19.6 + - - +
19B ALA* 5.9 1.2 - - - +
20B VAL* 3.1 39.0 - - + +
22B PRO* 3.8 20.5 - - - +
39B GLY 3.2 12.3 - - - +
40B ILE 3.1 4.7 + - - +
42B GLU* 1.3 76.2 - - + +
44B GLY* 1.3 61.0 + - - +
45B GLY 3.3 2.1 + - - -
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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