Contacts of the helix formed by residues 10 - 19 (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 LEU 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B PRO 3.2 0.8 + - - -
9B VAL* 1.3 92.0 - - + +
11B TYR* 1.3 58.7 + - - +
13B GLU* 3.2 25.3 - - + +
14B ALA* 2.9 27.9 + - - +
232B ILE* 4.5 2.7 - - + -
259B LEU* 3.9 22.2 - - + +
260B VAL* 4.6 4.7 - - - +
261B PRO* 3.4 31.9 - - + -
265B GLU* 5.6 1.6 - - - +
272B ALA* 5.8 0.4 - - + -
275B ALA* 4.3 5.4 - - + -
277B LEU* 3.4 43.7 - - + +
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Residues in contact with TYR 11 (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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7B VAL* 4.3 11.4 - - + +
8B PRO* 2.9 39.9 + - + +
9B VAL 2.9 3.8 + - - -
10B LEU* 1.3 76.6 - - - +
12B GLN* 1.3 89.1 + - + +
13B GLU* 3.9 0.2 + - - -
14B ALA* 3.3 1.9 + - - +
15B LEU* 2.9 50.6 + - + +
35B GLY 3.4 21.1 - - - -
36B HIS* 4.1 15.7 - + - -
38B ARG* 4.5 1.6 - - - +
39B GLY* 2.9 25.9 + - - -
42B GLU* 4.9 8.5 + - - -
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Residues in contact with GLN 12 (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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10B LEU 3.5 0.4 - - - -
11B TYR* 1.3 97.8 - - + +
13B GLU* 1.3 65.0 + - - +
15B LEU* 3.3 2.4 + - - +
16B ASP* 2.8 51.4 + - - +
43B ARG* 2.8 31.7 + - - +
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Residues in contact with GLU 13 (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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10B LEU* 3.2 38.0 - - + +
12B GLN* 1.3 81.2 + - - +
14B ALA* 1.3 62.9 + - - +
16B ASP* 3.3 7.4 + - - +
17B LEU* 3.0 30.1 + - - +
259B LEU* 3.7 31.0 - - + -
277B LEU* 4.5 3.4 - - + -
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Residues in contact with ALA 14 (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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10B LEU 2.9 17.7 + - - +
11B TYR 3.7 3.1 - - - +
13B GLU* 1.3 76.3 - - - +
15B LEU* 1.3 63.2 + - - +
17B LEU* 3.4 2.6 + - - +
18B LEU* 3.1 26.0 + - - +
36B HIS* 4.3 15.5 - - + +
94B LEU* 4.3 14.1 - - + -
230B VAL* 4.1 17.8 - - + +
232B ILE* 4.7 2.5 - - + -
277B LEU* 3.9 19.9 - - + +
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Residues in contact with LEU 15 (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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11B TYR* 2.9 61.2 + - + +
12B GLN* 3.6 2.0 - - - +
14B ALA* 1.3 78.7 - - + +
16B ASP* 1.3 60.1 + - - +
18B LEU* 3.4 11.5 - - + +
19B ALA* 3.3 14.7 + - - -
20B VAL* 4.3 5.8 + - + +
36B HIS* 3.8 13.7 - - + +
39B GLY* 3.8 5.4 - - - +
40B ILE* 3.8 39.7 - - + +
43B ARG* 3.6 43.5 + - - +
94B LEU* 5.9 0.4 - - + -
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Residues in contact with ASP 16 (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 36.9 + - - +
13B GLU* 3.6 6.9 - - - +
15B LEU* 1.3 69.4 - - - +
17B LEU* 1.3 61.2 + - + +
18B LEU 3.0 4.7 - - - -
19B ALA* 2.8 25.4 + - - +
43B ARG* 3.2 25.5 + - - +
228B ARG* 4.4 1.6 + - - -
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Residues in contact with LEU 17 (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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13B GLU 3.0 17.4 + - - +
14B ALA 3.9 1.1 - - - +
16B ASP* 1.3 77.7 - - + +
18B LEU* 1.3 56.2 + - - +
228B ARG* 2.8 41.0 + - - +
230B VAL* 3.9 15.5 - - + -
254B LEU* 4.3 22.7 - - + +
255B THR* 4.3 9.2 - - + -
259B LEU* 4.2 13.5 - - + -
277B LEU* 3.4 32.8 - - + -
279B ALA* 3.7 18.6 - - + -
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Residues in contact with LEU 18 (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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14B ALA 3.1 10.7 + - - +
15B LEU* 3.4 16.6 - - + +
16B ASP 3.0 0.6 - - - -
17B LEU* 1.3 78.2 - - - +
19B ALA* 1.3 69.0 + - - +
20B VAL* 3.2 6.6 + - + +
21B ARG* 5.4 0.9 + - - -
26B TYR* 4.1 25.1 - - + -
40B ILE* 3.5 37.7 - - + -
91B ASP 4.8 2.9 - - - +
92B GLY* 4.7 0.4 - - - -
93B ILE 3.8 24.7 - - - +
94B LEU* 4.2 16.6 - - + +
228B ARG* 4.2 14.1 - - - +
230B VAL* 3.3 30.3 - - + -
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Residues in contact with ALA 19 (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 3.3 3.7 + - - -
16B ASP* 2.8 17.1 + - - +
18B LEU* 1.3 80.5 - - - +
20B VAL* 1.3 64.3 + - - +
21B ARG* 3.5 21.0 + - - +
26B TYR* 3.9 0.3 + - - -
43B ARG* 5.9 0.9 - - - +
228B ARG* 4.1 20.9 - - + +
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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