Contacts of the strand formed by residues 32 - 40 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F LEU* 4.2 9.1 - - - +
31F GLN* 1.3 108.8 + - - +
33F PHE* 1.3 67.5 + - - +
98F TRP 3.5 5.6 - - - -
99F GLU* 3.6 24.9 - - - +
100F SER 3.7 1.7 + - - -
101F SER* 5.1 0.5 + - - -
161F ASP* 3.1 31.6 + - - +
162F SER* 3.9 11.0 - - - +
163F VAL* 4.2 10.5 - - + +
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Residues in contact with PHE 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LEU* 4.4 11.0 - - + -
32F ASN* 1.3 79.3 - - - +
34F THR* 1.3 71.5 + - - +
35F LEU* 4.1 8.5 - - + -
61F LEU* 3.6 42.0 - - + -
73F LEU* 4.2 7.6 - - + -
75F ILE* 3.7 17.3 - - + -
96F VAL* 3.9 20.6 - - + -
97F SER* 3.1 4.4 - - - -
98F TRP* 3.1 66.2 + + + +
125F VAL* 4.7 3.6 - - + -
159F MET* 4.1 20.9 - - + -
160F TRP 3.2 13.9 - - - +
161F ASP* 4.7 0.9 - - - -
162F SER 3.2 9.0 + - - +
163F VAL* 4.2 1.2 - - - +
182F ILE* 4.8 0.2 - - + -
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Residues in contact with THR 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F PHE* 1.3 76.8 + - - +
35F LEU* 1.3 62.9 + - - +
36F CYS* 4.2 7.6 - - - -
95F CYS* 4.8 0.2 - - + -
96F VAL 3.3 12.3 - - - +
97F SER* 3.5 7.0 - - - -
159F MET* 3.2 6.1 - - - +
160F TRP* 2.8 43.1 + - + -
162F SER 2.7 20.3 + - - -
163F VAL* 3.4 2.1 - - - -
164F LEU* 3.0 37.7 + - + -
169F ILE* 3.9 20.2 - - + -
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Residues in contact with LEU 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F PHE* 4.4 6.1 - - + -
34F THR* 1.3 75.3 - - - +
36F CYS* 1.3 62.2 + - - +
37F PHE* 3.9 16.6 - - + -
50F PHE* 3.4 60.1 - - + -
61F LEU* 5.1 3.8 - - + -
63F VAL* 4.0 14.1 - - + -
94F ILE 3.7 1.4 - - - +
95F CYS* 3.2 1.6 - - - -
96F VAL* 2.7 47.6 + - + +
157F LEU* 3.9 20.4 - - + -
158F TYR 3.4 15.7 - - - +
159F MET* 4.1 13.5 - - + -
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Residues in contact with CYS 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F THR* 4.2 6.5 - - - -
35F LEU* 1.3 75.3 - - - +
37F PHE* 1.3 64.2 + - - +
93F HIS* 4.0 9.0 - - - +
94F ILE 3.1 4.7 - - - -
95F CYS* 2.0 47.6 - - - -
156F ASP 3.3 2.6 - - - +
157F LEU* 3.2 2.4 - - - -
158F TYR* 2.7 39.3 + - + +
160F TRP* 3.6 31.0 - - + -
164F LEU* 4.8 0.4 - - - -
169F ILE* 4.5 2.0 - - - -
172F ALA* 4.1 8.1 - - + -
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Residues in contact with PHE 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LEU* 3.9 32.8 - - + -
36F CYS* 1.3 80.2 - - - +
38F ARG* 1.3 70.7 + - - +
39F ALA* 4.4 2.7 - - + -
49F LEU* 3.8 37.5 - - + -
50F PHE* 4.6 5.6 - - + -
63F VAL* 4.1 8.5 - - + -
92F VAL 4.1 0.3 - - - +
93F HIS* 3.6 9.4 + - - -
94F ILE* 2.9 72.6 + - + +
96F VAL* 5.6 0.7 - - + -
154F ILE* 4.6 7.9 - - + -
155F GLY 3.7 7.4 - - - +
156F ASP 3.4 9.6 - - - -
157F LEU* 3.8 24.0 - - + -
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Residues in contact with ARG 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 1.3 73.7 - - - +
39F ALA* 1.3 61.8 + - - +
92F VAL 3.4 12.1 - - - +
93F HIS* 3.8 23.1 - - + +
154F ILE* 3.3 7.8 - - - +
155F GLY* 2.8 38.7 + - - +
156F ASP* 2.8 33.6 + - - +
172F ALA 3.3 16.8 + - - -
173F TYR* 2.8 34.8 + - - -
174F GLN 4.4 0.6 - - - -
175F GLY* 3.9 12.1 - - - +
201F LEU* 4.9 4.0 - - + -
203F TRP* 3.6 17.9 - - + -
204F VAL* 3.7 38.5 - - + +
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Residues in contact with ALA 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 4.3 8.9 + - + -
38F ARG* 1.3 75.4 - - - +
40F TYR* 1.3 62.1 + - - +
41F SER* 4.3 0.9 - - - +
47F TYR* 6.2 0.4 - - - +
49F LEU* 3.9 28.0 - - + -
90F ALA 4.2 0.2 - - - +
91F PRO* 3.6 1.9 - - - +
92F VAL* 2.9 48.6 + - + +
94F ILE* 4.7 0.7 - - + -
150F PHE* 4.4 6.1 - - + -
153F GLU 3.3 8.7 - - - +
154F ILE* 4.4 1.8 - - + -
203F TRP* 3.8 3.4 - - - -
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Residues in contact with TYR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ALA* 1.3 75.9 - - - +
41F SER* 1.3 64.7 + - - +
89F PRO* 4.7 8.2 + - + +
90F ALA* 3.7 13.0 - - - -
91F PRO* 3.5 32.7 - - + +
152F GLY* 3.4 3.8 - - - -
153F GLU* 2.9 38.9 + - + +
203F TRP* 3.5 53.4 - + + +
83G LYS 5.2 2.4 + - - -
112G THR* 5.1 3.6 - - - +
113G PRO 2.8 29.7 + - - -
114G LEU* 3.4 14.5 - - - +
115G VAL* 3.6 36.6 + - + +
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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