Contacts of the helix formed by residues 54 - 69 (chain B) in PDB entry 2WA9
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 ASP 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B GLN* 3.7 3.6 - - - +
52B SER 3.7 1.6 + - - -
53B TYR* 1.3 77.0 - - - +
55B VAL* 1.3 68.5 + - + +
56B GLU* 3.5 24.7 - - - +
57B ARG* 3.0 28.6 + - - +
58B ALA* 3.0 19.3 + - - +
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Residues in contact with VAL 55 (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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44B ILE* 4.6 12.8 - - + -
48B GLN* 3.2 27.8 - - - +
54B ASP* 1.3 75.5 - - + +
56B GLU* 1.3 61.8 + - + +
58B ALA* 3.5 5.4 + - - +
59B THR* 2.7 35.9 + - - +
55E VAL* 5.1 14.8 - - + -
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Residues in contact with GLU 56 (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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54B ASP* 3.0 19.9 + - - +
55B VAL* 1.3 80.0 - - + +
57B ARG* 1.3 69.6 + - - +
59B THR* 3.0 12.8 + - - -
60B GLN* 2.2 32.3 - - - +
48E GLN* 4.9 10.1 - - - +
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Residues in contact with ARG 57 (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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53B TYR* 4.0 28.7 - - + -
54B ASP* 3.0 21.8 + - - +
56B GLU* 1.3 80.1 + - - +
58B ALA* 1.3 66.6 + - - +
60B GLN* 2.8 61.4 + - + +
61B LEU* 3.1 18.0 + - + +
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Residues in contact with ALA 58 (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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44B ILE* 4.4 13.8 - - + +
47B LEU* 3.3 36.2 - - + +
48B GLN* 4.4 11.2 - - + -
53B TYR* 4.3 4.8 - - + +
54B ASP 3.0 18.2 + - - +
55B VAL* 3.5 11.0 - - - +
57B ARG* 1.3 76.3 - - - +
59B THR* 1.3 57.2 + - - +
61B LEU* 4.8 1.3 - - - -
62B MET* 2.9 28.9 + - - +
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Residues in contact with THR 59 (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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44B ILE* 4.3 10.8 - - + +
55B VAL* 2.7 17.2 + - - +
56B GLU* 3.0 9.8 + - - -
57B ARG 3.0 1.2 - - - -
58B ALA* 1.3 75.2 - - - +
60B GLN* 1.3 68.2 - - - +
62B MET* 3.6 18.8 - - + +
63B LEU* 2.8 49.1 + - + +
41E GLU* 4.8 1.6 - - - +
44E ILE* 4.9 9.4 - - + -
55E VAL* 4.1 27.8 - - + +
59E THR* 5.6 2.5 - - - +
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Residues in contact with GLN 60 (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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56B GLU* 2.2 32.3 + - - +
57B ARG* 2.8 42.8 - - - +
59B THR* 1.3 76.3 - - - +
61B LEU* 1.3 64.9 + - + +
63B LEU* 3.3 3.3 + - - +
64B ALA* 2.9 28.0 + - - +
25C PRO* 5.0 2.1 - - - +
27C MET* 5.5 5.7 - - + +
77C THR* 5.2 12.1 - - + -
41E GLU* 2.8 45.0 + - + +
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Residues in contact with LEU 61 (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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47B LEU* 3.8 26.7 - - + -
53B TYR* 3.8 39.5 - - + +
57B ARG* 3.1 11.7 + - + +
58B ALA 3.9 1.3 - - - +
60B GLN* 1.3 84.1 - - + +
62B MET* 1.3 58.4 + - - +
64B ALA* 3.1 5.6 + - + +
65B VAL* 2.8 34.6 + - + +
71B ALA* 4.5 15.3 - - + -
72B ILE 4.6 11.0 - - - +
73B CYS* 4.4 9.2 - - - -
27C MET* 4.1 27.1 - - + -
75C VAL* 5.6 2.7 - - + +
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Residues in contact with MET 62 (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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40B MET* 3.7 53.6 - - + +
43B VAL* 3.9 29.8 - - + -
44B ILE* 4.2 14.8 - - + -
47B LEU* 4.2 0.2 - - - +
58B ALA 2.9 20.2 + - - +
59B THR* 3.2 21.3 + - + +
61B LEU* 1.3 78.8 - - - +
63B LEU* 1.3 80.3 + - + +
65B VAL* 3.1 3.0 + - - +
66B HIS* 2.8 26.3 + - - +
59E THR* 6.1 2.0 - - + +
1I LEU* 4.7 3.6 - - + +
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Residues in contact with LEU 63 (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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40B MET* 5.1 5.6 - - + -
59B THR* 2.8 50.0 + - + +
60B GLN 3.6 3.4 - - - +
62B MET* 1.3 91.5 - - + +
64B ALA* 1.3 52.7 + - - +
66B HIS* 3.2 1.9 + - - -
67B TYR* 2.7 67.1 + - + +
25C PRO* 4.1 7.4 - - + -
40E MET* 6.1 3.1 - - + -
41E GLU* 3.1 26.7 - - - +
44E ILE* 4.4 11.2 - - + -
59E THR* 4.9 18.2 - - + +
62E MET* 5.2 5.6 - - + -
3L THR* 5.7 1.3 - - - +
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Residues in contact with ALA 64 (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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60B GLN 2.9 14.1 + - - +
61B LEU* 3.1 14.1 + - - +
63B LEU* 1.3 72.7 - - - +
65B VAL* 1.3 59.8 + - - +
68B GLN* 2.8 34.7 + - - +
69B GLY 3.5 0.3 + - - -
70B LYS 3.7 3.7 - - - +
71B ALA* 4.0 12.1 - - + -
25C PRO* 3.2 23.0 - - + +
27C MET* 4.0 20.0 - - + -
108C ALA 4.3 1.8 - - - +
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Residues in contact with VAL 65 (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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32B LEU* 3.9 36.3 - - + +
33B VAL 4.0 3.6 - - - +
34B ASN* 3.3 34.6 - - - +
43B VAL* 4.9 1.1 - - + -
61B LEU* 2.8 24.1 + - + +
62B MET* 3.5 7.4 - - - +
64B ALA* 1.3 71.3 - - - +
66B HIS* 1.3 64.1 + - - +
69B GLY* 3.1 22.9 + - - -
70B LYS* 3.9 8.1 - - - +
71B ALA* 3.5 18.2 - - + -
99B LEU* 5.3 3.1 - - + -
1I LEU* 4.2 15.0 - - + -
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Residues in contact with HIS 66 (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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34B ASN* 3.7 16.7 + - - -
40B MET* 3.5 32.1 - - + +
62B MET* 2.8 14.0 + - - +
63B LEU* 3.5 9.4 - - - +
65B VAL* 1.3 78.8 - - - +
67B TYR* 1.3 97.6 + + + +
69B GLY 4.6 0.7 + - - -
1I LEU* 3.1 50.1 + - + +
2I LEU 5.0 0.8 - - - -
3I THR* 5.0 1.3 + - - -
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Residues in contact with TYR 67 (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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40B MET* 5.3 1.8 - - + +
63B LEU* 2.7 57.8 + - + +
66B HIS* 1.3 101.7 + + - +
68B GLN* 1.3 61.5 + - - +
69B GLY 3.4 1.3 - - - -
23C LYS* 2.6 39.5 + - + +
24C PRO* 3.4 16.6 - - + +
25C PRO* 4.3 0.7 - - + -
40E MET* 5.1 12.8 - - + -
59E THR* 5.7 0.7 - - - +
62E MET* 5.2 2.1 - - + +
63E LEU* 3.5 28.6 - - + +
67E TYR* 4.7 13.9 - - - -
3L THR* 3.5 20.0 - - - +
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Residues in contact with GLN 68 (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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64B ALA* 2.8 14.4 + - - +
67B TYR* 1.3 74.6 - - - +
69B GLY* 1.3 58.1 + - - +
70B LYS* 3.3 3.9 + - - +
24C PRO* 2.4 38.8 - - + +
25C PRO* 2.8 20.6 - - + +
26C SER* 4.0 6.2 + - - -
27C MET* 3.0 33.1 + - - +
105C LYS* 4.9 2.6 - - - -
107C GLY* 2.4 40.2 - - - +
108C ALA* 2.6 40.5 + - - -
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Residues in contact with GLY 69 (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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33B VAL* 3.8 6.4 - - - +
34B ASN* 3.0 33.2 + - - +
65B VAL 3.1 18.5 + - - -
67B TYR 3.4 2.2 - - - -
68B GLN* 1.3 78.4 - - - +
70B LYS* 1.3 63.8 + - - +
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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