Contacts of the strand formed by residues 91 - 102 (chain C) in PDB entry 1OPT
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 GLU 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C THR 5.6 1.6 - - - +
16C CYS* 3.4 18.4 - - + -
17C THR 2.9 40.7 + - - +
28C TRP* 4.7 1.7 - - - -
82C TYR 4.0 1.7 - - - +
84C CYS* 3.5 29.4 + - - +
86C VAL* 3.8 15.6 - - - +
89C GLN* 3.6 19.4 - - + +
90C LYS* 1.3 69.5 - - - +
92C GLU* 1.3 68.5 + - - +
93C VAL* 4.4 4.0 - - - +
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Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C LYS* 4.1 34.1 + - - +
2C LYS* 4.3 14.8 + - - +
81C THR* 3.4 26.1 - - + +
82C TYR 3.5 7.0 - - - +
83C ILE* 4.3 18.7 - - + +
90C LYS* 3.0 11.6 + - + +
91C GLU* 1.3 76.2 - - - +
93C VAL* 1.3 73.3 + - - +
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LYS* 3.4 21.1 - - + +
4C VAL* 3.9 22.4 - - + -
14C LEU* 4.3 17.0 - - + -
15C THR 5.9 0.2 - - - +
28C TRP* 3.7 25.6 - - + -
80C ASP 4.0 0.2 - - - +
81C THR* 3.2 5.1 - - - -
82C TYR* 2.6 54.9 + - + +
91C GLU 4.4 1.8 - - - +
92C GLU* 1.3 81.3 - - - +
94C GLN* 1.3 70.2 + - - +
95C LEU 3.9 0.3 + - - -
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Residues in contact with GLN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C LYS* 5.8 9.5 - - + +
2C LYS 2.9 12.3 + - - +
3C VAL* 3.7 22.9 - - + +
4C VAL* 3.0 27.4 + - - +
80C ASP* 4.0 4.3 - - - +
81C THR* 3.9 20.4 + - + +
93C VAL* 1.3 78.1 - - - +
95C LEU* 1.3 62.6 + - - +
96C LEU* 3.3 27.4 - - + +
164C ASN* 3.7 13.7 + - - +
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C VAL* 3.6 16.6 - - + +
6C GLY* 4.6 4.3 - - - +
12C VAL* 4.4 23.6 - - + -
14C LEU* 4.9 8.5 - - + -
71C ILE* 4.4 13.7 - - + -
74C LEU* 4.5 3.6 - - + -
78C ASP* 3.3 31.2 - - + +
79C SER* 3.3 5.5 - - - -
80C ASP* 2.8 38.1 + - - +
82C TYR* 3.7 17.7 - - + +
93C VAL* 6.0 0.2 - - + -
94C GLN* 1.3 74.9 - - - +
96C LEU* 1.3 81.9 + - - +
97C VAL* 4.2 15.5 - - + -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 4.5 7.9 - - + -
4C VAL 3.2 6.7 + - - -
5C LEU* 3.5 14.5 - - + -
6C GLY 3.1 22.3 + - - +
79C SER* 3.8 0.9 - - - -
94C GLN* 3.3 36.1 - - + +
95C LEU* 1.3 83.0 - - - +
97C VAL* 1.3 63.7 + - - +
98C PHE* 3.7 19.8 - - + -
121C PRO* 3.7 26.7 - - + -
123C GLY 5.1 3.6 - - - +
124C SER* 4.2 18.2 - - - -
163C GLN* 4.4 14.8 - - + -
164C ASN* 5.0 2.7 - - - +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLY 3.4 5.2 - - - +
8C LYS* 4.0 23.3 - - - +
74C LEU* 3.6 28.7 - - + -
75C LYS 3.2 35.9 - - - +
76C ILE* 4.1 11.1 - - + +
78C ASP* 4.3 0.2 - - + -
79C SER* 2.7 21.9 + - - +
95C LEU* 4.2 16.2 - - + -
96C LEU* 1.3 76.3 - - - +
98C PHE* 1.3 66.3 + - - +
119C GLU 3.8 1.6 - - - +
121C PRO* 3.3 25.1 - - - +
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Residues in contact with PHE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 4.0 17.7 - - + -
6C GLY 2.9 11.4 + - - +
7C LYS* 3.5 5.2 - - - -
8C LYS* 2.7 34.8 + - - -
76C ILE* 5.2 0.9 - - - -
96C LEU* 3.7 35.2 - - + -
97C VAL* 1.3 76.8 - - - +
99C GLY* 1.3 55.5 + - - +
118C LEU* 4.1 9.9 - - + -
119C GLU 3.3 15.0 - - - -
120C SER* 3.6 25.1 - - - -
121C PRO* 4.4 1.1 - - + -
124C SER* 4.6 1.3 - - - -
126C PRO* 3.7 25.8 - - + -
161C VAL* 4.1 16.2 - - + -
163C GLN* 3.9 19.7 - - + -
168C VAL* 4.6 4.7 - - + -
170C PHE* 3.5 20.6 - - + -
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Residues in contact with GLY 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS* 4.0 17.5 - - - -
98C PHE* 1.3 78.4 - - - +
100C LEU* 1.3 60.4 + - - -
101C THR* 5.1 3.5 - - - +
117C THR 3.7 1.4 - - - +
118C LEU* 3.2 5.4 - - - +
119C GLU* 2.6 47.8 + - - +
170C PHE* 4.2 3.4 - - - -
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C GLY* 1.3 71.7 - - - -
101C THR* 1.3 71.1 + - - +
116C LEU* 3.9 14.4 - - + +
117C THR 3.1 33.9 - - - +
118C LEU* 3.6 21.1 - - + +
128C VAL* 4.1 10.3 - - + -
130C CYS* 4.0 4.9 - - - -
144C LEU* 4.5 2.9 - - + -
159C CYS* 3.4 43.1 - - + -
161C VAL* 5.0 0.4 - - + -
170C PHE* 4.0 30.9 - - + -
172C ILE* 3.8 20.7 - - + +
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Residues in contact with THR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS* 6.6 0.2 - - + -
99C GLY 5.1 2.2 - - - -
100C LEU* 1.3 83.2 - - - +
102C ALA* 1.3 67.0 + - - +
103C ASN* 3.7 1.7 + - - -
116C LEU* 3.4 5.9 - - - -
117C THR* 2.7 52.9 + - - +
172C ILE* 5.2 3.6 - - - -
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C THR* 1.3 79.7 + - - +
103C ASN* 1.3 65.3 + - - +
104C SER 3.6 18.3 - - - +
106C THR* 6.5 0.4 - - + -
114C LEU* 4.2 12.8 - - + -
115C THR 3.3 7.2 - - - +
116C LEU* 3.8 18.5 - - + +
172C ILE* 4.7 15.0 - - + +
174C ILE* 4.7 4.5 - - + -
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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