Contacts of the helix formed by residues 6 - 20 (chain O) in PDB entry 2WWB
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 6 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4O GLN 3.3 13.5 - - - -
5O LYS* 1.4 81.4 + - - +
7O PHE* 1.4 64.6 + - - +
8O ARG* 3.5 19.9 + - - +
9O ILE* 3.9 14.9 + - - +
10O LYS* 4.4 4.0 + - - +
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Residues in contact with PHE 7 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K LEU* 5.9 6.3 - - + -
114K VAL* 3.7 22.7 - - + -
6O SER* 1.4 74.1 + - - +
8O ARG* 1.4 63.1 + - - +
10O LYS* 3.2 37.7 + - + +
11O GLN* 3.3 33.1 + - + +
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Residues in contact with ARG 8 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D U 5.4 10.3 + - - -
102D U 5.6 2.4 + - - -
88K MET* 4.6 28.1 - - + +
6O SER* 3.3 14.0 + - - +
7O PHE* 1.4 78.1 - - - +
9O ILE* 1.4 61.9 + - + +
11O GLN* 3.2 29.3 + - + +
12O LYS* 3.3 17.4 + - + +
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Residues in contact with ILE 9 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O ALA* 3.7 24.7 - - + -
4O GLN* 3.2 31.9 - - + +
5O LYS 4.5 3.1 - - - +
6O SER* 3.9 8.7 + - - +
7O PHE 3.3 0.6 - - - -
8O ARG* 1.4 74.7 - - + +
10O LYS* 1.4 61.4 + - - +
11O GLN 3.4 0.5 + - - -
12O LYS* 3.5 24.0 + - + +
13O MET* 3.5 33.1 + - + +
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Residues in contact with LYS 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O SER 4.4 2.8 + - - +
7O PHE* 3.2 35.5 + - + +
9O ILE* 1.4 76.3 - - - +
11O GLN* 1.4 57.4 + - - +
13O MET* 3.5 9.1 + - + +
14O ALA* 3.0 28.5 + - + +
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Residues in contact with GLN 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K MET* 4.8 15.0 - - + +
114K VAL* 3.6 37.8 - - + +
115K ARG 5.7 0.5 - - - +
118K GLY* 5.2 6.4 - - - +
7O PHE* 3.4 45.9 + - + +
8O ARG* 3.2 26.7 + - + +
10O LYS* 1.4 74.1 - - - +
12O LYS* 1.4 63.1 + - - +
14O ALA* 3.3 8.5 + - - +
15O LYS* 3.2 21.5 + - - +
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Residues in contact with LYS 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D A 3.0 24.9 + - - +
45D C 3.0 51.6 + - - +
101D U 5.9 2.9 - - - -
8O ARG* 3.3 10.3 + - + +
9O ILE* 3.5 26.7 - - + +
10O LYS 3.4 0.2 - - - -
11O GLN* 1.4 74.6 - - - +
13O MET* 1.4 74.4 + - + +
15O LYS* 3.6 7.2 + - - +
16O ALA* 3.2 25.3 + - - +
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Residues in contact with MET 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D C 5.3 11.0 - - - +
9O ILE* 3.5 30.2 + - + +
10O LYS* 3.7 9.9 - - + +
12O LYS* 1.4 84.9 - - + +
14O ALA* 1.4 58.1 + - - +
16O ALA* 3.3 10.5 + - - +
17O LYS* 3.1 26.7 + - - +
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Residues in contact with ALA 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K VAL* 5.9 3.4 - - + -
115K ARG 5.6 1.6 - - - +
116K PRO* 4.0 24.7 - - + +
10O LYS* 3.0 18.6 + - + +
11O GLN* 3.3 10.1 + - - +
13O MET* 1.4 74.7 - - - +
15O LYS* 1.4 62.4 + - - +
17O LYS* 3.6 13.2 + - - +
18O LYS 3.7 6.9 + - - -
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Residues in contact with LYS 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D C 5.3 0.4 - - - +
46D G 3.1 43.7 + - - +
47D C 3.1 25.9 + - - -
116K PRO* 3.5 13.8 - - - +
117K ASN* 3.2 29.8 + - - +
118K GLY* 3.9 13.7 - - - -
119K THR* 5.0 3.8 - - - +
11O GLN 3.2 13.2 + - - +
12O LYS* 3.9 9.4 - - - +
13O MET 3.4 0.2 - - - -
14O ALA* 1.4 73.8 - - - +
16O ALA* 1.4 59.1 + - - +
18O LYS* 3.1 8.1 + - + +
19O GLN* 2.9 38.3 + - + +
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Residues in contact with ALA 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D C 4.6 15.7 - - - +
46D G 3.5 13.7 - - - +
12O LYS 3.2 13.5 + - - +
13O MET* 3.3 16.5 + - - +
15O LYS* 1.4 77.9 - - - +
17O LYS* 1.4 60.1 + - - +
19O GLN* 3.3 9.3 + - - +
20O ASN* 3.3 14.2 + - - +
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Residues in contact with LYS 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O MET 3.1 12.0 + - - +
14O ALA* 3.9 11.0 - - - +
15O LYS 3.3 0.4 - - - -
16O ALA* 1.4 73.5 - - - +
18O LYS* 1.4 61.4 + - - +
20O ASN* 3.0 38.2 + - - +
22O PRO* 5.7 1.4 - - - +
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Residues in contact with LYS 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ARG* 5.5 14.7 - - - +
1677F G 5.9 1.8 - - - -
116K PRO* 3.8 24.2 - - + +
117K ASN* 5.7 6.3 - - - +
14O ALA 3.7 3.9 + - - +
15O LYS* 3.1 10.0 + - + +
17O LYS* 1.4 79.5 - - - +
19O GLN* 1.4 94.8 + - + +
20O ASN* 3.4 13.4 + - - +
22O PRO* 5.7 2.2 + - - +
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Residues in contact with GLN 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D G 3.6 27.1 - - - +
47D C 2.8 35.0 + - + +
52D A 5.3 0.2 + - - -
15O LYS* 2.9 28.1 + - + +
16O ALA 3.3 3.4 + - - +
18O LYS* 1.4 102.0 + - - +
20O ASN* 1.4 67.6 + - - +
21O ARG* 4.5 5.0 - - - +
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Residues in contact with ASN 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D A 4.2 0.9 + - - -
16O ALA 3.3 12.3 + - - +
17O LYS* 3.0 47.7 + - - +
18O LYS* 3.4 11.7 + - - +
19O GLN* 1.4 78.4 - - - +
21O ARG* 1.4 78.0 + - - +
22O PRO* 3.2 34.0 - - + +
37O TYR* 5.6 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