Contacts of the strand formed by residues 32 - 40 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30J LEU* 4.0 9.5 - - - +
31J GLN* 1.3 103.9 + - - +
33J PHE* 1.3 66.4 + - - +
98J TRP 3.4 4.9 - - - -
99J GLU* 3.3 28.2 - - - +
100J SER 3.8 1.6 + - - -
101J SER* 5.1 0.7 + - - -
161J ASP* 3.1 32.8 + - - +
162J SER* 3.9 11.6 - - - +
163J VAL* 4.1 9.2 - - + +
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Residues in contact with PHE 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J LEU* 4.3 12.1 - - + -
32J ASN* 1.3 78.2 - - - +
34J THR* 1.3 66.7 + - - +
35J LEU* 4.1 3.6 - - + -
61J LEU* 3.5 40.8 - - + -
73J LEU* 4.2 6.3 - - + -
75J ILE* 3.6 24.9 - - + -
96J VAL* 3.9 23.1 - - + -
97J SER* 3.1 5.9 - - - -
98J TRP* 3.0 61.2 + + + +
125J VAL* 4.6 3.8 - - + -
159J MET* 3.8 24.2 - - + -
160J TRP 3.2 13.5 - - - +
161J ASP* 4.8 0.4 - - - -
162J SER 3.3 9.3 + - - +
163J VAL* 4.5 0.3 - - - +
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Residues in contact with THR 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J PHE* 1.3 76.2 + - - +
35J LEU* 1.3 62.8 + - - +
36J CYS* 4.2 7.6 - - - -
95J CYS* 4.8 0.2 - - + -
96J VAL 3.3 10.8 - - - +
97J SER* 3.5 7.4 - - - -
159J MET* 3.2 5.5 - - - +
160J TRP* 2.8 45.9 + - + -
162J SER 2.6 22.2 + - - -
163J VAL* 3.4 1.9 - - - -
164J LEU* 2.9 39.4 + - + -
169J ILE* 3.9 17.3 - - + -
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Residues in contact with LEU 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J PHE* 4.5 6.5 - - + -
34J THR* 1.3 75.3 - - - +
36J CYS* 1.3 61.9 + - - +
37J PHE* 3.8 21.5 - - + -
50J PHE* 3.5 48.7 - - + -
61J LEU* 5.4 2.2 - - + -
63J VAL* 3.9 13.7 - - + -
94J ILE 3.8 0.5 - - - +
95J CYS* 3.1 2.8 - - - -
96J VAL* 2.7 46.8 + - + +
157J LEU* 3.7 27.1 - - + -
158J TYR 3.4 15.0 - - - +
159J MET* 4.0 14.4 - - + -
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Residues in contact with CYS 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J THR* 4.2 6.5 - - - -
35J LEU* 1.3 75.1 - - - +
37J PHE* 1.3 66.4 + - - +
93J HIS* 4.2 8.7 - - - +
94J ILE 3.1 4.9 - - - +
95J CYS* 2.0 45.3 - - - -
156J ASP 3.8 2.5 - - - +
157J LEU* 3.2 0.9 - - - +
158J TYR* 2.8 36.5 + - + +
160J TRP* 3.5 31.6 - - + -
164J LEU* 4.8 0.9 - - - -
169J ILE* 4.6 2.2 - - - -
172J ALA* 4.1 9.0 - - + -
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Residues in contact with PHE 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J LEU* 3.8 31.6 - - + -
36J CYS* 1.3 80.3 - - - +
38J ARG* 1.3 68.4 + - - +
39J ALA* 4.4 4.0 - - + -
49J LEU* 3.6 45.3 - - + -
50J PHE* 4.6 5.2 - - + -
63J VAL* 4.5 6.3 - - + -
92J VAL 4.1 0.2 - - - +
93J HIS* 3.6 9.1 + - - -
94J ILE* 2.8 69.6 + - + +
96J VAL* 5.7 0.4 - - + -
154J ILE* 4.5 8.3 - - + -
155J GLY 3.7 8.1 - - - +
156J ASP 3.2 10.3 - - - -
157J LEU* 3.8 24.5 - - + -
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Residues in contact with ARG 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J PHE* 1.3 73.4 - - - +
39J ALA* 1.3 61.1 + - - +
92J VAL 3.3 10.1 - - - +
93J HIS* 3.6 25.0 - - + +
154J ILE* 3.3 7.8 - - - +
155J GLY* 2.9 38.3 + - - +
156J ASP* 2.7 32.1 + - - +
172J ALA 3.3 17.0 + - - -
173J TYR* 2.8 33.7 + - - -
174J GLN 4.5 0.4 - - - -
175J GLY* 3.9 11.7 - - - +
201J LEU* 4.8 2.7 - - + -
203J TRP* 3.7 18.4 - - + -
204J VAL* 3.4 34.8 - - - +
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Residues in contact with ALA 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J PHE* 4.3 9.1 - - + -
38J ARG* 1.3 75.8 - - - +
40J TYR* 1.3 60.4 + - - +
41J SER* 4.2 0.9 - - - +
47J TYR* 6.1 0.7 - - - +
49J LEU* 4.3 18.2 - - + -
90J ALA 4.3 0.5 - - - +
91J PRO* 3.5 1.6 - - - +
92J VAL* 2.9 49.2 + - + +
94J ILE* 4.9 0.4 - - + -
150J PHE* 4.3 14.4 - - + -
153J GLU 3.2 8.3 - - - +
154J ILE* 4.3 4.5 - - + -
203J TRP* 3.8 3.1 - - - -
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Residues in contact with TYR 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F LYS 5.2 2.9 + - - -
112F THR* 5.1 4.2 - - - +
113F PRO 2.7 28.5 + - - -
114F LEU* 3.4 25.6 - - - +
115F VAL* 3.6 26.7 + - + +
39J ALA* 1.3 75.0 - - - +
41J SER* 1.3 62.2 + - - +
89J PRO* 4.8 8.1 + - + +
90J ALA* 3.7 12.3 - - - -
91J PRO* 3.4 37.7 - - + +
150J PHE* 4.6 0.2 - - - -
152J GLY* 3.3 3.3 - - - -
153J GLU* 2.8 38.4 + - + +
203J TRP* 3.6 51.8 - + + +
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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