Contacts of the strand formed by residues 88 - 94 (chain A) in PDB entry 2CHT
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 CYS 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ALA* 4.5 1.6 - - - -
10A THR 3.4 14.4 - - - +
11A THR* 4.1 1.1 - - + +
48A SER 3.9 0.9 - - - +
49A ALA* 3.6 1.9 - - - -
50A THR* 3.0 33.1 + - + +
53A LEU* 4.6 0.2 - - - -
78A GLU* 5.5 0.2 - - - +
85A LEU* 3.7 26.5 - - + +
86A LYS 2.8 11.0 + - - +
87A LYS* 1.3 75.5 - - - +
89A ILE* 1.3 64.9 + - - +
90A ARG* 3.1 49.9 + - - +
112A ALA* 4.8 0.2 - - - -
115A LEU* 4.3 5.2 - - - -
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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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9A ALA* 3.2 2.3 - - - -
10A THR* 2.9 44.9 + - + +
12A VAL* 4.1 15.5 - - + +
20A ILE* 3.8 23.8 - - + +
24A THR* 3.5 30.5 - - + +
27A LEU* 4.3 5.1 - - + +
47A LEU* 4.9 4.7 - - + -
48A SER 3.4 7.9 - - - +
49A ALA* 4.5 2.0 - - + -
53A LEU* 3.7 22.9 - - + -
58A PRO* 4.0 22.4 - - + -
87A LYS 4.8 2.0 - - - +
88A CYS* 1.3 74.7 - - - +
90A ARG* 1.3 68.8 + - - +
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Residues in contact with ARG 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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7A ARG* 3.4 17.5 - - - +
8A GLY 3.3 3.6 - - - -
9A ALA* 3.6 11.7 - - + -
47A LEU* 3.4 4.0 - - - +
48A SER* 2.8 43.1 + - - +
50A THR* 3.7 18.0 - - - +
78A GLU* 3.2 25.3 + - - +
85A LEU* 3.8 11.3 + - - +
88A CYS* 3.1 35.1 + - - +
89A ILE* 1.3 77.7 - - - +
91A VAL* 1.3 63.1 + - - +
115A LEU* 3.9 13.3 - - - +
203A TSA 2.9 49.5 + - - -
57C PHE* 3.7 14.8 - - - -
74C THR* 4.5 5.2 - - - +
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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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6A ILE 3.9 9.4 - - - +
7A ARG* 2.8 22.2 + - - -
8A GLY 2.8 19.4 + - - +
27A LEU* 3.5 33.0 - - + -
28A LEU* 4.4 10.8 - - + -
31A ILE* 3.7 23.6 - - + -
45A MET* 4.6 4.3 - - + -
46A LEU 3.2 11.7 - - - +
47A LEU* 3.7 22.4 - - + -
89A ILE* 5.3 1.3 - - + -
90A ARG* 1.3 74.6 - - - +
92A MET* 1.3 63.1 + - - +
93A MET* 4.1 10.8 - - + +
74C THR* 5.5 1.6 - - - -
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Residues in contact with MET 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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5A GLY* 4.3 5.6 - - - -
6A ILE 3.8 2.2 - - - -
7A ARG* 3.7 15.3 - - - -
45A MET* 3.4 1.9 - - - +
46A LEU* 2.9 44.1 + - + +
91A VAL* 1.3 75.0 - - - +
93A MET* 1.3 60.4 + - - +
94A THR* 4.2 1.3 + - - +
44C GLN* 3.9 35.9 - - + +
45C MET 3.7 17.0 - - - +
46C LEU* 4.5 7.4 - - + -
72C PRO* 3.6 47.1 - - + +
73C VAL 3.7 5.4 - - - -
74C THR* 4.0 16.8 - - + +
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Residues in contact with MET 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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4A ARG 3.7 0.3 - - - +
5A GLY* 3.0 4.2 - - - -
6A ILE* 2.7 71.7 + - + +
28A LEU* 5.1 6.7 - - - -
31A ILE* 3.7 21.1 - - + -
32A ILE* 5.3 2.0 - - - -
37A THR* 4.2 7.6 - - + +
42A VAL* 3.7 26.7 - - + -
44A GLN 3.9 1.8 - - - -
45A MET* 4.0 21.1 - - + +
68A TRP* 4.2 21.3 - - - -
91A VAL* 4.2 6.7 - - + -
92A MET* 1.3 75.7 - - - +
94A THR* 1.3 58.8 + - - +
95A VAL* 3.5 13.4 + - + -
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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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3A ILE* 3.7 31.6 - - + -
4A ARG 3.4 8.1 - - - +
5A GLY* 4.2 0.2 - - - -
42A VAL* 3.4 4.5 - - - +
43A VAL* 2.7 44.5 + - + -
44A GLN* 2.8 28.0 + - + +
92A MET* 4.8 2.3 + - - +
93A MET* 1.3 71.2 - - - +
95A VAL* 1.3 55.7 + - - +
43C VAL* 4.0 5.2 - - + -
44C GLN* 2.5 34.1 + - - +
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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