Contacts of the strand formed by residues 87 - 93 (chain A) in PDB entry 6S6A
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 VAL 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LYS 3.3 2.2 + - - -
10A VAL* 3.2 15.4 - - + -
11A LEU 2.9 30.7 + - - +
85A VAL* 3.5 9.0 - - - +
86A GLU* 1.3 85.0 - - + +
88A LEU* 1.3 61.5 + - - +
89A ILE* 4.0 11.9 - - + -
121A LYS* 3.4 21.5 - - + +
123A PHE* 3.6 25.6 - - + -
176A ILE* 4.4 5.8 - - + +
179A GLN* 6.1 0.2 - - + -
180A LEU* 3.3 39.7 - - + -
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Residues in contact with LEU 88 (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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11A LEU* 3.6 18.6 - - + +
13A MET* 3.9 28.5 - - + -
85A VAL* 4.2 0.6 - - - +
87A VAL* 1.3 73.1 - - - +
89A ILE* 1.3 70.6 + - - +
90A TYR* 4.5 12.1 - - + +
106A TYR* 5.4 1.8 - - + -
109A CYS* 4.3 22.2 - - + -
110A LEU* 4.8 5.8 - - + -
113A ILE* 3.9 32.3 - - + -
120A ALA* 5.1 0.8 - - + +
121A LYS 3.1 10.2 + - - +
122A ILE* 3.4 22.8 - - + -
123A PHE 2.9 30.7 + - - +
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Residues in contact with ILE 89 (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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10A VAL* 3.5 27.6 - - + -
11A LEU 2.9 10.0 + - - +
12A LEU* 3.5 18.1 - - + +
13A MET 3.1 24.1 + - - +
87A VAL* 4.0 9.2 - - + -
88A LEU* 1.3 76.0 - - - +
90A TYR* 1.3 60.3 + - - +
91A VAL* 4.8 0.7 - - + -
123A PHE* 3.5 7.0 - - + +
125A LEU* 3.8 32.5 - - + -
173A TRP* 3.2 37.2 - - + -
176A ILE* 3.9 25.1 - - + -
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Residues in contact with TYR 90 (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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13A MET* 3.1 24.9 - - + -
14A GLY* 3.8 8.8 - - - -
15A LYS* 4.5 2.1 + - - +
70A MET* 3.8 10.2 - - + +
88A LEU* 4.0 12.5 - - + -
89A ILE* 1.3 72.8 - - - +
91A VAL* 1.3 74.4 + - - +
92A PHE* 3.6 38.3 - + - -
102A ASP* 4.1 2.5 + - + -
105A TYR* 3.4 14.6 - - - +
106A TYR* 3.3 50.5 + + + -
109A CYS* 3.9 26.2 - - + -
122A ILE* 5.8 0.2 - - + -
123A PHE 2.8 14.2 + - - +
124A CYS* 3.5 4.9 - - - -
125A LEU* 2.9 25.2 + - - +
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Residues in contact with VAL 91 (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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12A LEU* 3.9 18.2 - - + -
13A MET 2.9 8.3 + - - +
14A GLY* 3.5 18.9 - - - -
15A LYS 4.2 2.1 + - - -
18A SER* 3.5 40.7 + - - +
19A GLY 4.7 0.4 - - - +
20A LYS* 3.9 20.6 - - + -
23A MET* 3.8 23.8 - - + -
90A TYR* 1.3 82.6 - - - +
92A PHE* 1.3 64.4 + - - +
125A LEU* 3.7 9.6 - - + +
127A HIS* 3.7 18.6 - - + -
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Residues in contact with PHE 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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18A SER* 4.4 0.2 - - - -
90A TYR* 3.6 34.8 - + - -
91A VAL* 1.3 81.0 - - - +
93A ASP* 1.3 61.9 - - - +
94A VAL* 5.3 0.7 - - - +
102A ASP* 4.4 26.0 - - + -
103A MET* 4.4 10.3 - - + -
106A TYR* 3.8 17.7 - + + -
124A CYS* 4.1 12.1 - - + -
125A LEU 2.9 17.2 + - - +
126A VAL* 4.5 10.8 - - + -
127A HIS* 2.9 32.2 + - - +
144A ARG* 6.0 3.1 - - - +
148A LEU* 3.5 46.0 - - + -
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Residues in contact with ASP 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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15A LYS* 4.6 13.0 - - + +
17A GLY 3.9 4.2 - - - +
18A SER* 4.1 18.6 - - - +
92A PHE* 1.3 71.1 - - - +
94A VAL* 1.3 66.3 + - - +
95A GLU* 2.9 29.0 + - - +
96A SER* 3.0 32.2 + - - +
99A LEU* 5.1 0.7 - - - +
102A ASP* 4.8 2.3 + - - +
127A HIS 4.2 2.2 - - - -
128A LYS* 2.9 41.8 + - - +
144A ARG* 4.2 4.6 + - - -
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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