Contacts of the strand formed by residues 64 - 72 (chain A) in PDB entry 2CGZ
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ILE* 4.3 17.6 - - + +
54A LEU* 4.2 21.1 - - + -
56A VAL* 4.5 0.2 - - + -
62A LEU* 4.0 30.9 + - + -
63A ARG* 1.3 79.7 - - - +
65A ILE* 1.3 68.6 + - - +
81A TYR 3.4 6.3 - - - +
82A THR* 4.8 0.4 - - - +
83A TRP* 4.0 3.7 - - - -
86A THR* 5.2 0.2 - - + -
88A VAL* 4.1 22.0 - - + -
91A MET* 4.1 16.2 - - - -
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Residues in contact with ILE 65 (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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25A ARG* 3.5 39.9 - - - +
51A ILE* 4.5 1.8 - - - -
64A VAL* 1.3 80.0 - - - +
66A ALA* 1.3 72.1 + - - +
67A ARG* 3.6 18.2 - - + +
79A SER 3.7 1.4 - - - +
81A TYR* 2.8 49.5 + - + +
83A TRP* 3.6 16.4 - - + -
91A MET* 3.3 13.3 - - - +
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Residues in contact with ALA 66 (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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49A LEU* 3.7 24.8 - - + +
50A SER 5.1 0.4 - - - +
51A ILE* 3.6 31.9 - - + +
65A ILE* 1.3 76.0 - - - +
67A ARG* 1.3 61.0 + - - +
68A LEU* 3.7 2.4 + - - +
79A SER 3.6 6.7 - - - -
93A ILE* 3.8 17.9 - - + -
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Residues in contact with ARG 67 (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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21A ASP* 2.9 40.4 + - - -
25A ARG* 5.0 5.1 - - - +
49A LEU* 3.6 1.1 - - - +
65A ILE* 3.6 19.6 - - + -
66A ALA* 1.3 73.0 - - - +
68A LEU* 1.3 63.9 + - - +
69A TYR* 3.6 42.3 + - + -
78A ALA* 3.2 7.1 - - - +
79A SER* 3.0 47.0 + - - +
81A TYR* 3.2 41.4 - - + -
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Residues in contact with LEU 68 (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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47A VAL* 3.4 39.0 - - + +
49A LEU* 3.6 19.3 - - + +
66A ALA 3.7 2.4 + - - +
67A ARG* 1.3 74.8 - - - +
69A TYR* 1.3 65.4 + - - +
70A SER 4.1 10.5 - - - +
71A VAL* 4.2 12.6 - - + -
76A PHE* 3.9 22.4 - - + -
77A LYS 3.9 13.0 - - - +
78A ALA* 4.1 4.5 - - + -
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Residues in contact with TYR 69 (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 VAL* 5.6 0.7 - - - +
30A GLU* 2.6 34.7 + - - -
67A ARG* 3.6 53.1 + - + -
68A LEU* 1.3 74.5 - - - +
70A SER* 1.3 64.1 + - - +
77A LYS* 3.0 58.3 + - + +
78A ALA* 4.4 2.2 - - - -
79A SER* 3.6 14.1 - - - -
81A TYR* 4.4 1.6 - - - -
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Residues in contact with SER 70 (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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68A LEU* 3.7 2.1 - - - +
69A TYR* 1.3 81.9 - - - +
71A VAL* 1.3 69.4 + - - +
72A SER 4.3 0.4 + - - -
76A PHE* 3.1 22.1 - - - +
77A LYS* 3.3 25.8 + - - +
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Residues in contact with VAL 71 (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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44A PRO* 3.4 15.8 - - + +
45A PRO* 3.2 35.4 - - + +
47A VAL* 3.9 30.5 - - + +
68A LEU* 4.2 13.2 - - + -
70A SER* 1.3 85.3 - - - +
72A SER* 1.3 71.7 + - - +
75A GLY 3.7 8.5 - - - +
76A PHE* 4.0 4.5 - - + -
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Residues in contact with SER 72 (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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44A PRO* 3.8 5.4 - - - -
45A PRO* 3.5 14.7 - - - +
70A SER* 4.3 0.6 - - - -
71A VAL* 1.3 74.4 - - - +
73A PRO* 1.3 73.8 - - - +
74A THR* 3.0 23.9 + - - +
75A GLY 3.0 26.9 + - - +
76A PHE* 4.8 0.8 - - - +
1101A NAG 6.1 2.2 - - - +
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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