Contacts of the strand formed by residues 91 - 100 (chain A) in PDB entry 3Q02
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 ILE 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A LEU* 4.9 10.1 - - + +
83A MET* 3.1 43.0 - - + +
89A ASP* 3.3 21.1 - - + +
90A GLU* 1.3 76.2 - - - +
92A SER* 1.3 67.2 + - - +
93A THR* 4.9 2.9 - - - -
145A LYS* 4.5 6.9 + - - -
169A LEU* 5.2 4.5 - - + -
170A TYR 3.6 7.4 - - - +
171A PHE* 3.6 26.0 - - + -
233A LEU* 4.6 8.5 - - + -
371A LEU* 3.7 30.7 - - + -
372A PHE* 4.8 15.9 - - + -
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Residues in contact with SER 92 (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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83A MET* 4.3 0.4 - - - -
90A GLU 4.1 0.2 - - - -
91A ILE* 1.3 75.5 - - - +
93A THR* 1.3 62.5 + - - +
143A HIS 3.5 4.9 + - - -
144A THR* 3.4 36.2 - - - +
145A LYS* 3.7 24.7 + - - +
169A LEU* 3.4 5.7 - - - +
170A TYR* 3.0 43.1 + - - +
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Residues in contact with THR 93 (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 TYR* 5.8 3.8 - - - -
38A GLY* 6.1 0.2 - - - -
79A TYR* 3.4 40.4 + - + +
83A MET* 3.8 20.3 - - + +
91A ILE* 4.9 0.4 - - - -
92A SER* 1.3 79.5 + - - +
94A THR* 1.3 68.2 + - - +
95A ASP* 4.8 5.9 + - - +
143A HIS* 3.6 9.9 + - - +
144A THR* 4.7 0.9 - - - -
167A ASN* 4.8 3.3 + - - -
168A ALA 3.5 4.5 - - - -
169A LEU* 3.5 24.8 - - - +
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Residues in contact with THR 94 (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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93A THR* 1.3 75.6 + - - +
95A ASP* 1.3 69.4 + - - +
139A TRP* 3.5 18.7 + - + +
140A VAL* 4.2 24.2 - - + -
143A HIS* 3.2 31.2 - - - +
144A THR* 4.4 2.2 - - + -
166A VAL* 5.0 2.9 - - + -
167A ASN* 3.3 8.5 + - - -
168A ALA* 3.0 44.8 + - + +
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY* 4.4 1.2 - - - +
41A SER* 3.2 21.7 + - - -
42A VAL* 3.1 21.7 - - + +
45A MET* 3.7 25.6 - - + +
79A TYR* 5.3 9.2 - - - -
93A THR* 4.8 6.8 + - - +
94A THR* 1.3 79.7 + - - +
96A ALA* 1.3 66.6 + - - +
119A SER* 5.4 6.1 + - - -
122A LYS* 5.7 1.0 - - - -
139A TRP* 4.5 5.5 + - - -
166A VAL 3.7 4.7 - - - -
167A ASN* 2.6 32.7 + - - -
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Residues in contact with ALA 96 (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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42A VAL* 4.7 2.0 - - - +
45A MET* 5.0 2.5 - - - -
94A THR* 5.3 0.7 - - + -
95A ASP* 1.3 78.6 - - - +
97A ILE* 1.3 64.3 + - - +
98A PHE* 3.5 25.3 - - + -
120A THR 5.7 2.9 - - - -
122A LYS* 5.2 6.1 - - + +
139A TRP* 3.9 18.6 - - + +
164A VAL 3.8 1.0 - - - +
165A LEU* 3.6 2.7 - - - +
166A VAL* 2.9 46.3 + - + +
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Residues in contact with ILE 97 (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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45A MET* 4.2 16.8 - - + -
46A LEU* 4.2 24.0 - - + +
49A THR* 4.4 9.9 - - + -
96A ALA* 1.3 78.3 - - - +
98A PHE* 1.3 63.0 + - - +
113A PHE* 4.1 30.5 - - + -
120A THR 5.2 3.4 + - - -
121A VAL* 3.6 23.8 - - + +
122A LYS* 3.0 26.9 + - - +
163A LEU* 3.6 27.8 - - + -
164A VAL 3.5 4.9 - - - +
165A LEU* 4.1 15.9 - - + -
309A LEU* 5.2 3.4 - - + -
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Residues in contact with PHE 98 (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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96A ALA* 3.5 25.6 - - + -
97A ILE* 1.3 76.4 - - - +
99A VAL* 1.3 61.0 + - - +
122A LYS* 3.3 32.1 - - + +
124A VAL* 4.2 18.4 - - + -
126A PHE* 4.0 20.3 - - + -
135A ILE* 4.9 4.9 - - + -
136A ILE* 3.6 43.5 - - + -
139A TRP* 4.1 30.5 - + + -
163A LEU* 3.3 7.1 - - - +
164A VAL* 2.8 48.1 + - + +
166A VAL* 4.0 12.8 - - + -
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Residues in contact with VAL 99 (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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98A PHE* 1.3 74.8 - - - +
100A GLN* 1.3 78.2 + - - +
103A LEU* 4.5 3.1 - - + -
105A LEU* 4.7 17.0 - - + -
121A VAL* 3.7 20.2 - - + -
122A LYS 3.0 12.1 + - - +
123A GLN* 3.4 17.6 - - + -
124A VAL 3.1 19.6 + - - -
126A PHE* 4.0 4.3 - - - -
162A ARG 3.4 11.9 - - - +
163A LEU* 4.0 9.0 - - + -
309A LEU* 4.4 6.5 - - + -
315A LEU* 4.1 26.0 - - + -
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Residues in contact with GLN 100 (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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99A VAL* 1.3 83.8 - - - +
101A ARG* 1.3 76.3 + - - +
102A ASP* 3.5 9.9 + - + +
103A LEU* 3.8 30.7 + - + +
105A LEU* 5.5 0.3 - - - +
123A GLN* 4.8 2.4 + - - -
124A VAL 3.4 2.9 - - - -
125A ASP* 3.3 17.7 + - - +
126A PHE* 2.9 44.7 - - - +
127A SER* 4.4 4.6 + - - +
159A GLN 5.5 1.4 + - - -
161A THR 3.9 2.8 + - - -
162A ARG* 3.0 38.7 + - + +
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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