Contacts of the helix formed by residues 77 - 83 (chain A) in PDB entry 2CLS
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.7 22.5 - - + -
74A TYR* 3.4 11.2 - - + +
76A ASN* 1.3 77.8 - - - +
78A ARG* 1.3 68.4 + - - +
79A PRO* 3.4 2.7 - - - -
80A LEU* 3.2 29.7 + - + +
81A CYS 4.5 0.2 + - - -
46B VAL* 3.4 30.3 - - + +
47B PHE* 3.9 15.9 - - + -
74B TYR* 4.1 11.2 - - + -
77B VAL* 3.7 28.8 - - + +
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Residues in contact with ARG 78 (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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19A VAL* 4.1 2.2 - - - -
47A PHE* 3.8 13.7 - - + -
68A THR* 3.8 33.7 - - + -
69A SER 3.0 21.7 + - - -
71A SER 2.6 32.3 + - - -
74A TYR* 3.0 17.6 + - - +
75A ASP* 2.8 28.1 + - - +
77A VAL* 1.3 76.5 - - - +
79A PRO* 1.3 69.8 - - + +
80A LEU 2.9 1.4 + - - -
81A CYS* 3.0 22.3 + - - -
82A TYR* 3.8 13.2 + - + +
106A LYS* 5.0 0.2 - - - +
107A TRP* 3.6 22.4 - - - -
110A GLU* 2.9 33.0 + - - +
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Residues in contact with PRO 79 (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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75A ASP 3.1 22.4 - - - +
76A ASN 4.2 4.0 - - - +
77A VAL 3.5 4.7 - - - +
78A ARG* 1.3 91.8 - - + +
80A LEU* 1.3 60.7 + - - +
81A CYS 3.1 0.4 - - - -
82A TYR* 3.1 45.2 + - + +
110A GLU* 4.4 14.1 - - + +
114A TYR* 3.7 20.6 - - + -
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Residues in contact with LEU 80 (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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76A ASN 5.4 1.3 + - - +
77A VAL* 3.2 33.9 + - + +
78A ARG 2.9 1.6 + - - -
79A PRO* 1.3 78.2 - - - +
81A CYS* 1.3 60.3 + - - +
82A TYR 3.3 0.2 - - - -
83A SER* 3.4 12.8 + - - -
114A TYR* 5.7 0.7 - - - -
47B PHE* 4.7 14.8 - - + -
66B TRP* 4.6 13.9 - - + -
77B VAL* 4.1 15.7 - - + +
78B ARG* 5.4 0.2 - - - -
80B LEU* 3.0 50.0 - - + +
81B CYS* 3.6 26.5 - - - -
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Residues in contact with CYS 81 (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* 3.1 28.8 + - - +
17A VAL* 3.5 9.6 - - + +
47A PHE* 3.5 32.1 - - - -
66A TRP* 3.3 34.3 - - + -
68A THR* 3.7 15.5 - - - -
78A ARG 3.0 20.6 + - - -
80A LEU* 1.3 77.0 - - - +
82A TYR* 1.3 61.4 + - - +
83A SER 3.3 1.6 - - - -
77B VAL* 4.3 6.7 - - + -
80B LEU* 4.3 4.3 - - - -
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Residues in contact with TYR 82 (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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17A VAL* 4.0 19.5 - - + -
19A VAL* 3.5 33.4 - - + +
78A ARG* 3.8 10.4 - - + -
79A PRO* 3.1 35.3 + - + +
81A CYS* 1.3 77.2 - - - +
83A SER* 1.3 63.6 + - - +
84A ASP 3.3 0.9 + - - -
85A SER* 2.8 27.9 + - - +
88A VAL* 4.3 17.7 - - + -
107A TRP* 4.7 0.5 - - - -
110A GLU* 2.4 45.4 + - + +
111A ILE* 4.5 15.7 - - + +
114A TYR* 3.6 39.8 - - + -
118A THR* 5.2 1.3 + - + +
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Residues in contact with SER 83 (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* 2.6 33.1 + - - -
80A LEU 3.4 16.2 + - - -
81A CYS 3.3 0.8 - - - -
82A TYR* 1.3 76.0 - - - +
84A ASP* 1.3 74.9 + - - +
85A SER 3.1 0.3 + - - -
114A TYR* 2.9 26.2 + - - -
80B LEU* 4.5 12.5 - - - +
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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