Contacts of the strand formed by residues 32 - 40 (chain G) in PDB entry 2A3W
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 ASN 32 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU* 3.6 10.1 - - - +
31G GLN* 1.3 114.5 + - - +
33G PHE* 1.3 67.2 + - - +
98G TRP 3.4 6.7 - - - +
99G GLU* 3.7 22.5 - - - +
100G SER* 3.8 1.9 + - - -
101G SER* 5.0 1.2 + - - -
161G ASP* 3.1 32.5 + - - +
162G SER* 3.8 11.9 - - - +
163G VAL* 4.2 8.7 - - + +
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Residues in contact with PHE 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU* 4.3 10.5 - - + -
32G ASN* 1.3 77.8 - - - +
34G THR* 1.3 72.4 + - - +
35G LEU* 4.0 9.2 - - + -
61G LEU* 3.5 41.3 - - + -
73G LEU* 4.2 7.4 - - + -
75G ILE* 3.6 14.6 - - + -
96G VAL* 3.9 19.7 - - + -
97G SER* 3.2 4.9 - - - -
98G TRP* 3.0 70.7 + + + +
125G VAL* 4.8 2.9 - - + -
159G MET* 3.9 21.3 - - + -
160G TRP 3.2 13.5 - - - +
162G SER 3.2 10.6 + - - +
163G VAL* 4.3 0.2 - - - -
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Residues in contact with THR 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G PHE* 1.3 76.8 + - - +
35G LEU* 1.3 64.2 + - - +
36G CYS* 4.2 6.5 - - - -
96G VAL 3.3 10.8 - - - +
97G SER* 3.4 6.0 - - - -
159G MET* 3.2 5.9 - - - +
160G TRP* 2.8 44.2 + - + -
162G SER 2.6 20.9 + - - -
163G VAL* 3.3 1.7 - - - -
164G LEU* 2.8 30.7 + - + -
169G ILE* 3.8 29.2 - - + -
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Residues in contact with LEU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G PHE* 4.0 9.8 - - + -
34G THR* 1.3 75.3 - - - +
36G CYS* 1.3 61.7 + - - +
37G PHE* 3.7 21.4 - - + -
50G PHE* 3.5 53.4 - - + -
61G LEU* 5.5 0.4 - - + -
63G VAL* 3.8 16.2 - - + -
94G ILE 3.8 0.9 - - - +
95G CYS* 3.2 1.6 - - - -
96G VAL* 2.7 48.0 + - + +
157G LEU* 3.8 18.6 - - + -
158G TYR 3.4 14.1 - - - +
159G MET* 4.0 15.5 - - + -
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Residues in contact with CYS 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G THR* 4.2 7.2 - - - -
35G LEU* 1.3 74.0 - - - +
37G PHE* 1.3 67.2 + - - +
93G HIS* 4.1 9.2 - - - +
94G ILE 3.1 4.9 - - - +
95G CYS* 2.0 46.0 - - - -
156G ASP 3.9 2.9 - - - +
157G LEU* 3.2 0.9 - - - +
158G TYR* 2.8 36.6 + - + +
160G TRP* 3.6 29.8 - - + -
164G LEU* 4.7 0.7 - - - -
169G ILE* 4.5 2.5 - - - -
172G ALA* 4.1 8.5 - - + -
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Residues in contact with PHE 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G LEU* 3.7 33.2 - - + -
36G CYS* 1.3 80.2 - - - +
38G ARG* 1.3 74.2 + - - +
39G ALA* 4.5 2.7 - - + -
49G LEU* 3.5 45.1 - - + -
50G PHE* 4.5 6.3 - - + -
63G VAL* 4.3 6.5 - - + -
92G VAL 4.1 0.2 - - - +
93G HIS* 3.6 7.2 + - - -
94G ILE* 2.9 65.1 + - + +
96G VAL* 5.7 0.7 - - + -
154G ILE* 4.5 8.3 - - + -
155G GLY 3.7 7.2 - - - +
156G ASP 3.4 11.2 - - - -
157G LEU* 3.7 24.2 - - + -
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Residues in contact with ARG 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G PHE* 1.3 74.1 - - - +
39G ALA* 1.3 62.2 + - - +
92G VAL 3.3 10.3 - - - +
93G HIS* 3.8 26.6 - - + +
154G ILE* 3.2 8.3 - - - +
155G GLY 2.8 38.1 + - - +
156G ASP* 2.7 33.2 + - + +
172G ALA 3.5 14.8 + - - -
173G TYR* 2.8 36.3 + - - -
174G GLN 4.6 0.4 - - - -
175G GLY* 3.9 11.5 - - - +
201G LEU* 4.7 3.1 - - + +
203G TRP* 3.7 16.6 - - + -
204G VAL* 3.5 39.8 - - - +
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Residues in contact with ALA 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G PHE* 4.3 8.9 + - + -
38G ARG* 1.3 75.5 - - - +
40G TYR* 1.3 60.9 + - - +
41G SER* 4.2 0.7 - - - -
47G TYR* 6.1 0.9 - - - +
49G LEU* 4.3 24.2 - - + -
90G ALA 4.3 0.3 - - - +
91G PRO* 3.5 1.7 - - - +
92G VAL* 3.0 46.9 + - + +
94G ILE* 4.7 1.1 - - + -
150G PHE* 4.3 7.9 - - + -
153G GLU 3.2 9.4 - - - +
154G ILE* 4.3 3.8 - - + -
203G TRP* 3.8 4.0 - - - -
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Residues in contact with TYR 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G ALA* 1.3 75.6 - - - +
41G SER* 1.3 63.0 + - - +
89G PRO* 4.7 7.0 - - + +
90G ALA* 3.8 13.5 - - - -
91G PRO* 3.5 33.6 - - + +
150G PHE* 4.5 0.2 - - - -
152G GLY* 3.4 3.6 - - - -
153G GLU* 2.9 37.2 + - + +
203G TRP* 3.5 54.5 - + + -
83H LYS 5.3 1.7 + - - -
112H THR* 4.9 4.5 - - - +
113H PRO 2.7 28.8 + - - -
114H LEU* 3.5 14.7 - - - +
115H VAL* 3.5 38.2 + - + +
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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