Contacts of the helix formed by residues 5 - 19 (chain A) in PDB entry 2WA2
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 SER 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ALA* 1.3 69.5 + - - +
7A PRO* 3.5 7.4 - - - +
8A THR* 3.2 14.0 + - - -
9A LEU* 2.9 32.4 + - - +
236A THR* 3.9 22.3 + - - +
240A ARG* 4.7 7.9 + - - -
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Residues in contact with ALA 6 (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 SER* 1.3 79.6 + - - +
7A PRO* 1.4 71.6 - - + +
9A LEU* 3.9 4.0 - - - +
10A GLY 3.0 21.0 + - - -
189A TYR* 3.7 10.1 - - - +
194A LEU* 3.5 24.5 - - + -
232A MET* 5.0 6.7 - - + +
235A VAL* 4.5 12.6 - - + -
236A THR* 3.8 21.1 + - - +
239A SER* 4.6 1.3 + - - -
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Residues in contact with PRO 7 (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 SER* 3.7 4.7 - - - +
6A ALA* 1.4 93.8 - - + +
8A THR* 1.3 57.3 + - - +
10A GLY* 4.1 0.2 - - - -
11A GLU* 2.9 51.2 + - - +
189A TYR* 3.2 23.0 - - + +
190A SER* 4.8 1.1 - - - -
191A CYS* 3.7 32.3 - - + +
194A LEU* 4.4 2.7 - - + -
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Residues in contact with THR 8 (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 SER* 3.2 15.1 + - - -
7A PRO* 1.3 79.7 - - - +
9A LEU* 1.3 60.4 + - + +
11A GLU* 3.5 8.2 - - - +
12A ILE* 2.9 52.1 + - + +
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Residues in contact with LEU 9 (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 SER* 2.9 23.7 + - - +
6A ALA* 4.0 2.5 - - - +
8A THR* 1.3 75.3 - - + +
10A GLY* 1.3 66.0 + - - +
12A ILE* 3.3 17.1 + - + +
13A TRP* 3.0 22.9 + - - +
236A THR* 3.8 20.9 - - + +
239A SER* 3.9 14.5 - - - -
240A ARG* 3.5 55.4 - - + +
243A LEU* 3.9 23.6 - - + +
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Residues in contact with GLY 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 ALA 3.0 10.5 + - - -
9A LEU* 1.3 77.3 - - - +
11A GLU* 1.3 57.3 + - - +
13A TRP* 3.3 12.2 + - - +
14A LYS* 2.8 28.2 + - - +
189A TYR* 3.5 33.0 - - - -
219A HIS* 4.5 0.7 - - - -
239A SER* 3.7 11.9 + - - -
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Residues in contact with GLU 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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7A PRO* 2.9 38.8 + - - +
8A THR* 3.5 7.8 - - - +
10A GLY* 1.3 75.0 - - - +
12A ILE* 1.3 65.3 + - - +
14A LYS* 3.6 5.4 - - - +
15A ARG* 3.1 38.9 + - + +
155A ALA* 5.1 9.2 - - + -
189A TYR* 3.7 14.0 - - + -
190A SER* 5.8 1.9 - - - -
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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 THR* 2.9 38.9 + - + +
9A LEU* 3.6 20.9 - - + +
11A GLU* 1.3 73.4 - - + +
13A TRP* 1.3 56.0 + - - +
15A ARG* 3.2 5.9 + - - +
16A LYS* 2.8 57.2 + - + +
243A LEU* 4.1 11.7 - - + -
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Residues in contact with TRP 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 LEU 3.0 14.0 + - - +
10A GLY* 3.3 16.1 + - - +
12A ILE* 1.3 75.1 - - - +
14A LYS* 1.3 92.0 + - + +
16A LYS* 3.7 2.3 - - - +
17A LEU* 2.7 49.8 + - + +
28A TYR* 3.2 29.7 + - - -
158A GLU* 5.4 1.1 - - - -
189A TYR* 3.9 5.8 - - - -
216A ASN 3.3 19.9 + - - -
217A SER 3.7 17.7 - - - -
218A THR* 3.8 7.0 - - - -
219A HIS* 3.4 43.5 - + + -
239A SER* 5.0 2.7 - - - +
242A LEU* 3.6 25.9 - - + +
243A LEU* 3.5 18.3 - - + +
246A MET* 4.4 8.0 - - + +
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Residues in contact with LYS 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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10A GLY 2.8 17.1 + - - +
11A GLU* 3.6 8.1 - - - +
12A ILE 3.2 0.4 - - - -
13A TRP* 1.3 98.9 - - + +
15A ARG* 1.3 60.2 + - + +
17A LEU* 3.3 11.7 + - + +
18A ASN* 3.0 40.4 + - - +
151A SER* 5.3 2.6 - - - -
152A ASN 2.8 30.6 + - - +
153A PRO* 3.4 23.7 - - - +
155A ALA* 4.1 13.9 - - + +
158A GLU* 3.0 23.6 + - - -
189A TYR* 3.7 19.1 - - - +
217A SER 5.5 1.4 + - - -
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Residues in contact with ARG 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 GLU* 3.1 27.5 + - + +
12A ILE* 3.8 5.6 - - - +
14A LYS* 1.3 78.2 - - + +
16A LYS* 1.3 63.5 + - + +
18A ASN* 3.3 10.5 + - - +
19A GLN* 3.2 31.6 + - - +
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Residues in contact with LYS 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* 2.8 39.9 + - + +
13A TRP 3.7 0.2 - - - +
15A ARG* 1.3 75.8 - - + +
17A LEU* 1.3 66.0 + - - +
19A GLN* 3.1 27.7 + - - +
20A LEU* 3.5 12.0 + - - +
243A LEU* 4.1 8.5 - - + -
246A MET* 3.6 39.2 - - + +
247A GLU* 6.4 2.0 - - - -
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Residues in contact with LEU 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 TRP* 2.7 43.6 + - + +
14A LYS* 3.3 14.1 + - + +
16A LYS* 1.3 72.2 - - - +
18A ASN* 1.3 65.8 + - - +
20A LEU* 3.1 33.2 + - + +
25A PHE* 4.0 24.6 - - + -
28A TYR* 3.6 36.3 - - + -
217A SER* 3.5 34.1 - - - +
246A MET* 4.1 3.3 - - - -
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Residues in contact with ASN 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 LYS* 3.0 31.2 + - - +
15A ARG* 3.7 9.0 - - - +
16A LYS 3.2 0.4 - - - -
17A LEU* 1.3 81.7 - - - +
19A GLN* 1.3 58.8 + - + +
20A LEU 3.3 1.7 - - - +
153A PRO* 2.9 45.6 + - - +
18B ASN* 5.6 3.1 - - + -
153B PRO* 3.2 24.3 - - - +
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Residues in contact with GLN 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 ARG* 3.2 18.1 + - - +
16A LYS* 3.1 20.8 + - - +
18A ASN* 1.3 77.5 - - + +
20A LEU* 1.3 63.0 + - + +
21A ASP 3.6 1.9 + - - -
24A GLU* 4.3 3.5 - - - +
152B ASN* 4.3 7.8 + - - +
153B PRO* 3.7 15.6 - - - +
154B THR* 4.2 19.7 + - - +
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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