Contacts of the helix formed by residues 9 - 19 (chain A) in PDB entry 2D2W
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 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A SER* 3.1 5.3 - - - -
8A TYR* 1.3 81.7 - - - +
10A GLN* 1.3 60.1 + - - +
11A LEU 3.5 0.2 - - - -
12A ILE 4.1 0.7 - - - -
13A VAL* 3.1 6.2 - - - +
54A ASN* 5.0 0.4 - - - +
58A ASN* 3.0 26.7 - - - +
60A TYR* 2.8 29.5 - - + +
61A PHE* 2.9 28.8 - - - -
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Residues in contact with GLN 10 (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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6A TYR* 3.0 22.3 - - - +
7A SER* 2.8 35.2 + - - -
9A ALA* 1.3 76.7 - - - +
11A LEU* 1.3 66.9 + - - +
12A ILE 3.1 1.1 - - - -
13A VAL* 3.1 21.9 + - - +
14A GLN* 3.2 16.3 + - - +
60A TYR* 5.4 0.4 - - - -
87A LEU 4.9 1.8 - - - -
90A GLN* 3.0 46.6 + - + +
91A ALA* 3.1 22.4 + - - +
93A ARG 3.2 16.4 + - - -
95A ARG* 5.4 2.3 - - - -
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Residues in contact with LEU 11 (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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5A PRO* 5.1 1.1 - - + -
6A TYR* 3.5 36.6 - - + +
7A SER 2.6 20.4 + - - +
8A TYR* 3.9 23.1 - - + -
10A GLN* 1.3 81.2 + - - +
12A ILE* 1.3 59.9 + - - +
14A GLN* 3.7 3.8 + - - +
15A ALA* 3.5 11.3 + - - +
29A ILE* 3.6 26.9 - - + -
32A HIS* 3.6 14.7 + - + -
33A ILE* 3.3 34.8 - - + -
40A TYR* 5.2 0.4 - - + -
47A TRP* 3.8 19.5 - - + -
51A ILE* 4.1 1.1 - - + -
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Residues in contact with ILE 12 (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 TYR 3.0 23.6 - - - +
9A ALA 4.0 0.2 + - - -
10A GLN 3.1 0.8 - - - -
11A LEU* 1.3 77.1 - - - +
13A VAL* 1.3 57.1 + - - +
15A ALA* 2.7 29.2 + - + +
16A ILE* 2.9 10.4 + - + +
29A ILE* 2.8 31.2 - - + -
51A ILE* 3.2 23.3 - - + -
55A LEU* 3.4 10.3 - - + -
61A PHE* 3.3 18.6 - - + -
77A TRP* 3.0 46.2 - - + -
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Residues in contact with VAL 13 (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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9A ALA 3.1 19.1 - - - +
10A GLN* 3.1 8.4 + - - +
12A ILE* 1.3 75.9 - - - +
14A GLN* 1.3 56.5 + - - +
16A ILE* 4.2 0.2 - - - -
17A SER* 2.5 55.8 + - - +
60A TYR* 4.3 0.4 - - + -
61A PHE* 3.2 16.1 - - + -
87A LEU* 3.0 48.9 - - + +
88A VAL* 3.7 8.1 - - + -
91A ALA* 3.7 19.3 - - + -
92A PHE* 5.9 0.7 - - + -
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Residues in contact with GLN 14 (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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6A TYR* 3.4 33.7 - - - -
10A GLN* 3.2 21.2 + - - +
11A LEU 4.0 1.3 + - - +
12A ILE 3.2 0.6 - - - -
13A VAL* 1.3 78.0 - - - +
15A ALA* 1.3 56.7 + - - +
17A SER* 4.7 0.9 - - - -
18A SER* 2.4 42.7 + - - +
32A HIS* 3.5 22.7 + - + +
91A ALA* 2.5 48.4 + - + +
92A PHE* 4.6 11.0 - - + -
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Residues in contact with ALA 15 (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 LEU 3.5 0.2 + - - -
12A ILE* 2.7 20.5 + - + +
14A GLN* 1.3 73.8 - - - +
16A ILE* 1.3 60.0 + - - +
18A SER* 3.7 0.3 - - - -
19A ALA* 2.8 24.1 + - - +
24A LEU* 3.0 22.3 - - + +
29A ILE* 3.3 28.3 - - + -
32A HIS* 3.1 26.3 + - - +
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Residues in contact with ILE 16 (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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12A ILE* 2.9 16.7 + - + +
13A VAL 4.1 0.4 - - - +
15A ALA* 1.3 72.3 - - - +
17A SER* 1.3 71.5 + - - +
19A ALA* 2.9 14.0 + - - +
22A ARG* 3.1 24.2 - - - +
23A GLN* 3.2 2.9 - - - -
24A LEU* 3.0 50.8 - - + +
61A PHE* 3.0 40.8 - - + -
77A TRP* 3.5 13.7 - - + -
78A ARG* 3.1 6.3 - - - -
79A ILE* 3.1 23.3 - - + +
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Residues in contact with SER 17 (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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13A VAL* 2.5 50.1 + - - +
14A GLN* 4.7 0.4 - - - -
16A ILE* 1.3 74.7 - - - +
18A SER* 1.3 58.1 + - - -
19A ALA 4.2 0.5 - - - +
20A GLN 5.0 0.3 - - - +
21A ASP 3.8 11.3 - - - +
22A ARG* 4.2 6.1 - - - +
79A ILE* 3.4 11.3 - - - +
84A GLU* 3.1 29.2 + - - +
88A VAL* 5.0 2.0 - - - -
92A PHE* 6.6 0.2 - - - -
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Residues in contact with SER 18 (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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14A GLN* 2.4 38.6 + - - +
15A ALA 4.1 0.2 - - - -
16A ILE 3.1 0.6 - - - -
17A SER* 1.3 76.7 - - - +
19A ALA* 1.3 70.7 + - - +
92A PHE* 5.6 4.0 - - - -
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Residues in contact with ALA 19 (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 ALA 2.8 19.1 + - - +
16A ILE 2.9 10.6 + - - +
17A SER 4.2 1.6 - - - +
18A SER* 1.3 89.8 - - - +
20A GLN* 1.3 79.0 + - + +
23A GLN 3.8 2.9 - - - +
24A LEU* 3.3 31.4 - - + -
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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