Contacts of the strand formed by residues 98 - 107 (chain A) in PDB entry 6ISB
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 GLY 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A MET* 5.3 0.6 - - - +
92A LEU 4.0 0.5 - - - +
94A THR* 2.8 48.1 + - - +
96A PRO 3.2 1.8 - - - -
97A GLN* 1.3 80.8 - - - +
99A THR* 1.3 63.0 + - - -
100A TRP* 4.0 1.9 + - - -
29B GLN* 4.3 1.8 - - - -
31B GLU* 3.6 18.2 - - - -
44B ILE* 3.7 6.7 - - - -
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Residues in contact with THR 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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91A SER* 5.3 3.4 - - - +
92A LEU 3.4 9.0 - - - +
93A TYR* 3.2 39.1 - - + +
98A GLY* 1.3 73.0 - - - -
100A TRP* 1.3 72.3 + - - +
101A GLN* 5.7 1.8 - - + -
29B GLN* 4.6 1.4 + - - -
31B GLU* 3.9 7.0 + - - -
33B PHE* 5.3 5.7 - - - -
93B TYR* 3.3 22.3 + - + +
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Residues in contact with TRP 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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3A VAL 5.8 1.6 - - - +
4A LEU* 3.7 32.5 - - + -
5A TRP* 3.8 33.4 - + + -
19A CYS* 5.9 1.1 - - - -
20A VAL 5.7 0.4 - - - -
21A TYR* 4.1 5.0 - - + +
22A PRO* 3.5 24.9 - - + -
24A MET* 3.1 39.9 - - + +
91A SER* 3.7 1.6 - - - -
92A LEU* 2.7 74.6 + - + +
94A THR* 4.6 6.5 - - + +
98A GLY 5.7 0.2 - - - -
99A THR* 1.3 79.6 - - - +
101A GLN* 1.3 82.7 + - - +
102A LYS* 4.1 9.4 - - + -
173A PHE* 3.8 21.5 - + - -
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Residues in contact with GLN 101 (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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3A VAL* 3.4 31.2 - - - +
4A LEU 3.1 24.9 + - - -
5A TRP 3.8 0.9 + - - -
89A SER* 2.6 28.0 + - - +
90A CYS 3.6 3.6 - - - +
91A SER* 4.0 10.1 + - - +
99A THR* 5.7 2.7 - - + -
100A TRP* 1.3 87.1 - - - +
102A LYS* 1.3 68.2 + - - +
103A VAL* 4.2 5.4 - - + -
95C TYR* 2.4 40.0 + - - -
96C PRO* 5.6 5.1 - - - +
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Residues in contact with LYS 102 (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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5A TRP* 3.2 66.4 - - + +
7A THR* 3.8 27.8 + - - +
18A GLU* 2.8 45.0 + - - +
19A CYS* 4.4 12.6 - - + +
20A VAL 5.2 0.2 - - - +
89A SER* 3.5 2.3 - - - -
90A CYS* 2.8 47.1 + - + +
100A TRP* 4.1 9.6 - - + -
101A GLN* 1.3 72.6 - - - +
103A VAL* 1.3 63.8 + - - +
104A ILE* 4.0 8.5 + - + +
154A GLN* 5.5 1.6 + - - +
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Residues in contact with VAL 103 (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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3A VAL* 3.9 29.4 - - + -
5A TRP 2.8 9.0 + - - +
6A HIS* 3.2 24.7 - - + +
7A THR 3.0 23.6 + - - -
35A ILE* 4.2 4.5 - - + -
87A TYR* 4.0 15.9 - - + -
88A TYR 3.2 11.7 - - - +
101A GLN* 4.1 6.5 - - + -
102A LYS* 1.3 75.1 - - - +
104A ILE* 1.3 64.9 + - - +
26C ILE* 3.7 26.2 - - + -
95C TYR* 4.2 15.5 - - + -
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Residues in contact with ILE 104 (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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7A THR* 3.4 23.8 - - - +
9A VAL* 4.3 11.4 - - + -
17A LEU* 3.8 32.1 - - + -
18A GLU 3.2 28.3 - - - +
32A TRP* 3.6 26.5 - - + -
86A GLY 3.8 0.7 - - - +
87A TYR* 3.5 0.5 - - - -
88A TYR* 2.6 47.2 + - + +
90A CYS* 5.3 0.2 - - + -
102A LYS* 4.1 14.4 - - + +
103A VAL* 1.3 81.7 - - - +
105A GLN* 1.3 68.3 + - - +
106A VAL* 5.0 0.4 - - + +
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Residues in contact with GLN 105 (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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6A HIS* 4.8 4.8 - - + -
7A THR 2.9 9.4 + - - +
8A SER* 3.2 20.8 + - - +
9A VAL* 2.9 28.2 + - - +
86A GLY* 3.5 9.1 - - - +
87A TYR* 3.3 51.6 + - + -
103A VAL* 4.3 0.6 - - - +
104A ILE* 1.3 72.6 - - - +
106A VAL* 1.3 67.1 + - - +
107A VAL* 3.5 24.6 + - + +
47C PRO* 5.1 7.1 - - - +
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Residues in contact with VAL 106 (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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9A VAL* 3.4 7.9 - - + +
11A PHE* 3.7 23.8 - - + +
15A MET* 3.6 30.3 - - + -
17A LEU* 3.6 31.2 - - + -
84A ASP 4.0 1.1 - - - +
85A VAL* 3.3 18.4 - - - +
86A GLY* 2.7 35.2 + - - +
88A TYR* 3.7 18.6 - - + -
104A ILE* 5.0 0.2 - - + -
105A GLN* 1.3 75.9 + - - +
107A VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 107 (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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8A SER* 4.9 5.6 - - - -
9A VAL 3.0 7.2 + - - +
10A PRO* 3.3 2.8 - - - +
11A PHE* 2.7 34.2 + - - -
85A VAL* 4.7 3.1 - - - -
105A GLN* 3.5 41.7 - - + +
106A VAL* 1.3 74.5 - - - +
108A GLN* 1.3 57.6 + - - +
109A SER* 3.7 9.6 - - - -
112A PHE* 3.7 35.9 - - + -
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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