Contacts of the strand formed by residues 32 - 40 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.5 10.5 - - - +
31A GLN* 1.3 94.0 - - - +
33A PHE* 1.3 65.7 + - - +
98A TRP 3.5 4.3 - - - -
99A GLU* 3.4 27.7 - - - +
100A SER 3.9 0.9 + - - -
101A SER* 5.2 0.5 + - - -
161A ASP* 3.2 32.2 + - - +
162A SER* 3.8 10.6 - - - +
163A VAL* 4.1 11.0 - - + +
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Residues in contact with PHE 33 (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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30A LEU* 4.1 12.6 - - + -
32A ASN* 1.3 76.8 - - - +
34A THR* 1.3 73.0 + - - +
35A LEU* 4.0 4.7 - - + -
61A LEU* 3.5 41.5 - - + -
73A LEU* 4.1 7.2 - - + -
75A ILE* 3.6 25.4 - - + -
96A VAL* 3.9 23.6 - - + -
97A SER* 3.2 2.4 - - - -
98A TRP* 3.1 59.3 + + + +
125A VAL* 4.8 3.6 - - + -
159A MET* 4.0 21.5 - - + -
160A TRP 3.2 14.6 - - - +
162A SER 3.2 10.3 + - - +
163A VAL* 4.3 0.5 - - - -
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Residues in contact with THR 34 (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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33A PHE* 1.3 76.7 + - - +
35A LEU* 1.3 64.4 + - - +
36A CYS* 4.2 8.1 - - - -
96A VAL 3.3 12.3 - - - +
97A SER* 3.5 6.8 - - - -
159A MET* 3.2 5.7 - - - +
160A TRP* 2.8 44.8 + - + -
162A SER 2.7 20.4 + - - -
163A VAL* 3.4 1.6 - - - -
164A LEU* 2.9 42.3 + - + -
169A ILE* 4.0 13.9 - - + -
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Residues in contact with LEU 35 (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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33A PHE* 4.4 6.5 - - + -
34A THR* 1.3 75.0 - - - +
36A CYS* 1.3 61.3 + - - +
37A PHE* 3.8 20.0 - - + -
50A PHE* 3.5 48.5 - - + -
61A LEU* 5.2 2.5 - - + -
63A VAL* 3.8 15.9 - - + -
94A ILE 3.8 1.0 - - - +
95A CYS* 3.1 2.8 - - - -
96A VAL* 2.8 45.1 + - + +
157A LEU* 3.7 27.6 - - + -
158A TYR 3.4 15.3 - - - +
159A MET* 4.0 13.2 - - + -
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Residues in contact with CYS 36 (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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34A THR* 4.2 7.0 - - - -
35A LEU* 1.3 75.4 - - - +
37A PHE* 1.3 65.4 + - - +
93A HIS* 4.2 8.1 - - - +
94A ILE 3.1 4.3 - - - -
95A CYS* 2.0 46.7 - - - -
156A ASP 3.3 3.1 - - - +
157A LEU* 3.2 1.2 - - - +
158A TYR* 2.8 36.1 + - + +
160A TRP* 3.6 30.7 - - + -
164A LEU* 4.6 4.3 - - - -
169A ILE* 4.6 0.2 - - - -
172A ALA* 4.4 9.4 - - + -
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Residues in contact with PHE 37 (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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35A LEU* 3.8 26.9 - - + -
36A CYS* 1.3 80.4 - - - +
38A ARG* 1.3 76.2 + - - +
39A ALA* 4.4 2.9 - - + -
49A LEU* 3.8 38.6 - - + -
50A PHE* 4.7 5.2 - - + -
63A VAL* 4.3 7.4 - - + -
93A HIS* 3.6 5.2 + - - -
94A ILE* 2.8 75.4 + - + +
96A VAL* 5.7 0.4 - - + -
154A ILE* 4.7 8.7 - - + -
155A GLY 3.6 7.2 - - - +
156A ASP 3.2 9.6 - - - -
157A LEU* 3.7 27.6 - - + -
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Residues in contact with ARG 38 (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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37A PHE* 1.3 73.7 - - - +
39A ALA* 1.3 61.1 + - - +
92A VAL 3.3 10.1 - - - +
93A HIS* 3.6 30.2 - - + +
154A ILE* 3.3 8.1 - - - +
155A GLY 2.8 35.8 + - - +
156A ASP* 2.7 33.8 + - + +
172A ALA 3.5 14.3 + - - -
173A TYR* 2.9 34.9 + - - -
174A GLN 4.6 0.2 - - - -
175A GLY* 3.9 11.9 - - - +
201A LEU* 4.8 2.9 - - - -
203A TRP* 3.6 16.8 - - + -
204A VAL* 3.6 40.3 - - - +
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Residues in contact with ALA 39 (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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37A PHE* 4.4 7.2 - - + -
38A ARG* 1.3 75.5 - - - +
40A TYR* 1.3 60.9 + - - +
41A SER* 4.2 0.9 - - - +
47A TYR* 6.1 0.4 - - - +
49A LEU* 3.9 28.3 - - + -
90A ALA 4.2 0.7 - - - +
91A PRO* 3.5 1.2 - - - +
92A VAL* 2.9 46.6 + - + +
94A ILE* 4.9 0.6 - - + +
150A PHE* 4.3 4.7 - - + -
153A GLU 3.2 9.6 - - - +
154A ILE* 4.2 7.0 - - + -
203A TRP* 3.9 3.5 - - - -
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Residues in contact with TYR 40 (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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39A ALA* 1.3 75.3 - - - +
41A SER* 1.3 62.9 + - - +
89A PRO* 4.6 6.5 + - + +
90A ALA* 3.7 13.0 - - - -
91A PRO* 3.5 35.1 - - + +
152A GLY* 3.4 2.9 - - - -
153A GLU* 2.8 38.2 + - + +
203A TRP* 3.5 55.0 - + + +
83B LYS 5.2 2.9 + - - -
112B THR* 5.0 4.0 - - - +
113B PRO 2.7 29.6 + - - -
114B LEU* 3.5 13.2 - - - +
115B VAL* 3.6 38.3 + - + +
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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