Contacts of the helix formed by residues 10 - 19 (chain B) in PDB entry 2W9B
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 TYR 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 PHE 3.5 1.8 + - - -
9B ASP* 1.3 91.2 - - + +
11B PHE* 1.3 55.1 + - - +
12B TYR 3.4 1.8 - - - -
13B ALA* 3.2 6.1 + - + -
14B GLN* 2.7 68.3 + - + +
17B GLU* 3.8 19.7 + - - -
45B THR* 4.6 7.9 - - - +
46B ALA 3.6 20.2 - - - +
47B ASN* 3.9 20.9 - - + -
48B TYR* 3.4 34.1 - + + -
51B ARG* 4.3 15.6 - - - +
139B THR* 4.3 8.9 + - - +
159B LYS* 5.8 2.2 - - - +
160B PRO* 4.9 3.6 - - + -
14D DOC 6.5 1.1 - - - -
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Residues in contact with PHE 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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8B PHE* 3.5 32.7 + + + +
9B ASP 2.7 11.0 + - - -
10B TYR* 1.3 69.8 - - - +
12B TYR* 1.3 76.4 + + + +
14B GLN* 4.5 2.5 - - - +
15B VAL* 2.5 53.3 + - + +
45B THR* 5.8 0.4 - - + +
81B TYR* 3.4 37.7 - - + -
84B VAL* 4.6 7.2 - - + -
85B SER* 3.8 15.9 - - - -
88B ILE* 5.0 3.4 - - + -
104B ILE* 3.6 21.8 - - + -
105B ASP* 3.6 33.9 - - + +
138B ILE* 5.0 4.9 - - + -
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Residues in contact with TYR 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 TYR 3.2 1.2 + - - -
11B PHE* 1.3 105.2 - + + +
13B ALA* 1.3 53.0 + - - +
15B VAL* 3.2 3.8 + - - +
16B GLU* 2.8 32.4 + - - +
30B VAL* 3.9 12.8 - - + -
44B ALA* 3.9 8.3 - - + -
45B THR* 3.3 30.6 - - + +
76B MET* 3.3 37.0 - - + +
78B LYS* 3.4 25.6 + - + +
81B TYR* 3.5 24.3 - + + -
104B ILE* 4.0 22.3 - - + +
105B ASP* 4.5 4.5 - - - -
14D DOC 6.3 2.5 - - + -
5F O2G 6.1 1.1 - - + -
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Residues in contact with ALA 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 TYR* 3.2 6.8 + - + +
12B TYR* 1.3 75.9 - - - +
14B GLN* 1.3 61.9 + - - +
16B GLU* 2.7 21.1 + - - +
17B GLU* 3.2 16.0 + - - +
28B VAL* 3.9 8.1 - - + +
30B VAL* 3.5 20.5 - - + +
45B THR* 3.9 7.7 + - - +
46B ALA 4.2 0.2 - - - -
47B ASN* 3.7 37.7 - - + +
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Residues in contact with GLN 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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8B PHE* 4.5 0.8 - - - +
9B ASP* 2.8 21.8 + - - +
10B TYR* 2.7 44.9 + - + +
11B PHE* 3.9 3.7 - - - +
13B ALA* 1.3 70.6 - - - +
15B VAL* 1.4 63.1 + - - +
17B GLU* 2.8 20.5 + - + +
18B VAL* 3.1 13.6 + - + +
137B LYS 4.1 0.8 - - - +
138B ILE* 2.8 31.7 - - + +
139B THR* 2.5 54.5 + - - +
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Residues in contact with VAL 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 PHE* 2.5 58.6 + - + +
12B TYR 3.3 3.8 - - - +
14B GLN* 1.4 68.5 - - - +
16B GLU* 1.3 64.3 + - - +
17B GLU 3.0 0.7 + - - -
18B VAL* 3.2 14.6 + - + +
19B LEU* 3.4 16.3 + - + +
80B VAL* 4.1 13.0 - - + -
81B TYR* 3.7 22.2 - - + -
84B VAL* 4.1 25.4 - - + -
138B ILE* 4.2 13.5 - - + -
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Residues in contact with GLU 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 TYR 2.8 16.2 + - - +
13B ALA* 2.7 19.0 + - - +
15B VAL* 1.3 74.5 - - - +
17B GLU* 1.3 61.7 + - - +
19B LEU* 3.5 8.6 + - - +
20B ASN* 3.3 14.6 + - - +
23B LEU* 3.6 10.7 - - - +
28B VAL* 4.6 3.1 - - + -
30B VAL* 3.8 17.7 - - + -
74B LEU* 3.0 38.7 - - + +
75B PRO* 5.0 1.6 - - - -
77B ARG* 3.5 33.2 + - - +
80B VAL* 5.6 0.3 - - - +
81B TYR* 3.1 26.7 + - + +
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Residues in contact with GLU 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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10B TYR* 3.8 18.1 + - - -
13B ALA 3.2 17.1 + - - +
14B GLN* 2.8 12.1 + - + +
16B GLU* 1.3 74.9 - - - +
18B VAL* 1.3 59.2 + - + +
19B LEU 2.8 5.4 - - - -
20B ASN 2.6 25.4 + - - -
21B PRO* 2.8 21.7 - - + +
23B LEU* 3.9 9.9 - - + -
24B LYS* 3.6 51.1 - - + +
25B GLY 5.1 0.4 + - - -
28B VAL* 3.4 20.4 - - + +
47B ASN* 4.0 17.5 + - - +
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Residues in contact with VAL 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 GLN* 3.1 14.6 + - + +
15B VAL* 3.2 11.2 + - + +
17B GLU* 1.3 78.9 - - + +
19B LEU* 1.3 69.1 + - + +
20B ASN 3.7 0.2 + - - -
21B PRO* 4.6 5.2 - - - +
84B VAL* 6.0 4.0 - - + -
136B GLU* 4.3 12.6 - - - +
137B LYS* 2.9 41.7 - - + +
138B ILE* 3.5 19.7 - - + -
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Residues in contact with LEU 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 VAL* 3.4 16.1 + - + +
16B GLU* 4.0 7.9 - - - +
17B GLU 2.8 1.2 - - - -
18B VAL* 1.3 98.8 - - + +
20B ASN* 1.3 60.7 + - - +
21B PRO* 4.3 2.0 - - - -
77B ARG* 3.9 24.2 - - - +
80B VAL* 3.3 34.1 - - + -
84B VAL* 5.5 4.3 - - + -
87B ARG* 6.3 1.1 - - - +
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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