Contacts of the helix formed by residues 34 - 43 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 2.8 39.6 + - + -
32A GLY 3.2 1.4 + - - -
33A GLY* 1.3 81.1 - - - +
35A GLY* 1.3 63.4 + - - +
36A HIS 3.4 2.2 - - - -
37A ALA* 3.8 7.2 - - + +
38A ARG* 3.0 25.6 + - + +
60A ALA* 5.2 2.2 - - + -
63A LEU* 4.0 17.7 - - + -
65A LEU* 4.3 11.9 - - + -
68A LEU* 4.8 3.4 - - + -
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PRO* 3.5 17.7 - - - -
11A TYR* 3.3 15.9 - - - -
33A GLY 3.3 3.0 - - - -
34A ALA* 1.3 78.5 - - - +
36A HIS* 1.3 62.9 + - - +
38A ARG* 3.6 14.8 + - - +
39A GLY 3.7 1.9 + - - -
3142A SAM 3.0 19.0 + - - -
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Residues in contact with HIS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 3.6 19.0 - - + +
9A VAL 2.9 29.1 + - - -
11A TYR* 4.1 21.9 - + - -
14A ALA* 4.1 10.0 - - + +
15A LEU* 4.0 7.2 - - + +
28A ASP* 4.0 4.7 + - - +
35A GLY* 1.3 72.5 - - - +
37A ALA* 1.3 66.8 + - - +
39A GLY* 2.9 13.2 + - - -
40A ILE* 3.1 15.3 + - - +
94A LEU* 3.5 31.5 - - + +
96A ASP* 3.5 28.5 - - + +
232A ILE* 4.1 7.5 - - + +
3142A SAM 2.9 27.7 + - - +
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 3.4 12.1 + - - +
31A LEU* 3.6 31.4 - - + -
34A ALA* 3.4 10.7 + - + +
35A GLY 3.3 0.4 - - - -
36A HIS* 1.3 78.7 - - - +
38A ARG* 1.3 63.5 + - - +
40A ILE* 2.9 13.6 + - - +
41A LEU* 2.9 26.7 + - + +
47A VAL* 4.1 15.2 - - + +
65A LEU* 5.6 0.2 - - + -
68A LEU* 4.8 5.8 - - + -
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 4.3 2.7 - - - +
33A GLY 5.1 2.8 + - - -
34A ALA 3.0 22.8 + - - +
35A GLY* 3.7 9.9 - - - +
37A ALA* 1.3 74.3 - - - +
39A GLY* 1.3 57.4 + - - +
41A LEU* 3.2 11.7 + - - +
42A GLU* 2.9 37.7 + - + +
63A LEU* 4.1 28.3 + - - +
65A LEU* 3.4 40.9 - - + +
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Residues in contact with GLY 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 2.9 29.9 + - - -
15A LEU* 3.8 7.2 - - - -
35A GLY 3.7 0.6 + - - -
36A HIS 2.9 10.0 + - - -
38A ARG* 1.3 80.4 - - - +
40A ILE* 1.3 60.8 + - - +
42A GLU* 3.5 6.4 + - - +
43A ARG* 3.2 35.1 + - - +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.1 7.9 - - + -
18A LEU* 3.7 30.1 - - + -
20A VAL* 4.1 15.7 - - + -
26A TYR* 3.7 36.6 - - + -
27A VAL 5.5 0.9 - - - +
28A ASP* 5.0 9.0 - - + -
36A HIS 3.1 14.3 + - - +
37A ALA* 2.9 11.2 + - - +
39A GLY* 1.3 74.0 - - - +
41A LEU* 1.3 67.6 + - - +
43A ARG* 3.0 12.0 + - - +
44A GLY 3.3 0.2 + - - -
45A GLY* 3.2 20.5 + - - -
47A VAL* 3.5 25.4 - - + -
94A LEU* 4.9 9.2 - - + -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ALA* 2.9 20.5 + - + +
38A ARG* 3.6 8.3 - - - +
40A ILE* 1.3 75.9 - - - +
42A GLU* 1.3 53.8 + - + +
44A GLY* 2.7 26.7 + - - -
45A GLY 3.6 19.2 - - - +
47A VAL* 3.9 11.7 - - + -
65A LEU* 3.8 35.9 - - + -
66A PRO* 3.4 27.6 - - + +
67A GLY* 3.6 22.2 - - - +
68A LEU* 4.0 6.7 - - + +
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.6 20.4 + - - -
38A ARG* 2.9 23.7 + - + +
39A GLY* 3.6 5.5 - - - +
40A ILE 3.2 0.2 - - - -
41A LEU* 1.3 76.8 - - + +
43A ARG* 1.3 63.0 + - + +
44A GLY 3.1 2.8 + - - -
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 4.7 3.6 + - - -
12A GLN* 3.4 33.7 + - - +
15A LEU* 3.3 42.2 + - - +
16A ASP* 4.0 6.5 + - - +
20A VAL* 3.7 37.7 - - + +
21A ARG* 4.7 0.5 - - - -
22A PRO* 3.8 19.2 - - - +
39A GLY* 3.2 19.3 + - - +
40A ILE 3.0 9.2 + - - +
42A GLU* 1.3 83.1 + - + +
44A GLY* 1.3 59.9 + - - +
45A GLY 3.5 1.8 + - - -
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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