Contacts of the strand formed by residues 93 - 98 (chain J) in PDB entry 2EWC
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 ALA 93 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16I THR 3.4 13.7 - - - +
19I VAL* 3.8 6.0 - - + +
26I TYR* 3.6 22.9 - - + +
27I LEU 3.7 5.4 - - - +
28I ASN* 3.5 23.3 - - - +
64J VAL 3.0 14.6 + - - +
65J GLN* 3.2 7.1 - - + -
66J MSE 2.8 23.4 + - - -
92J PRO* 1.3 75.9 - - - +
94J ARG* 1.3 60.2 + - - +
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Residues in contact with ARG 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I ARG 2.5 29.9 + - - -
14I GLY 2.8 21.0 + - - -
15I HIS* 3.8 14.3 - - + +
27I LEU 5.0 0.2 + - - -
28I ASN* 2.8 23.6 + - - +
29I TYR* 3.0 37.4 + - + -
115I ASP* 4.9 1.3 - - - +
65J GLN* 4.1 4.5 - - - +
66J MSE 3.0 26.5 - - + +
68J CYS* 3.9 10.8 - - - -
76J ILE* 4.7 5.3 - - - +
79J MSE 3.8 25.7 - - - +
80J GLU* 4.0 17.3 + - - +
83J ILE* 3.4 25.3 - - - +
92J PRO* 4.7 2.7 + - - +
93J ALA* 1.3 78.4 - - - +
95J LYS* 1.3 63.4 + - - +
96J SER* 4.6 5.9 + - - -
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Residues in contact with LYS 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H LYS* 5.9 1.3 - - - +
29I TYR* 4.2 20.9 - - + -
67I ASP* 2.5 38.1 + - - +
69I LEU* 4.0 30.7 - - + -
95I LYS* 5.8 0.9 - - - +
97I ILE* 5.3 4.7 - - - -
113I GLN* 5.4 0.2 - - - +
115I ASP* 2.7 32.0 + - - +
65J GLN* 4.2 1.4 - - - +
66J MSE 3.2 3.3 + - - +
67J ASP* 2.9 35.4 + - - +
68J CYS* 2.9 25.8 + - - -
94J ARG* 1.3 78.9 - - - +
96J SER* 1.3 64.2 + - - +
97J ILE* 4.5 11.7 - - + -
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Residues in contact with SER 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I TYR* 5.4 2.0 - - - -
69I LEU* 3.9 12.0 - - - +
99I THR* 4.8 2.4 + - - +
100I GLU 5.3 1.0 - - - +
101I PHE* 5.5 2.9 - - - -
113I GLN* 4.9 4.2 + - - +
68J CYS* 3.2 10.4 - - - +
70J PHE* 3.6 23.5 - - - -
73J VAL* 4.2 5.2 - - - +
76J ILE* 3.7 27.9 - - - +
79J MSE 3.8 11.4 - - - +
94J ARG* 4.6 5.0 + - - -
95J LYS* 1.3 78.7 + - - +
97J ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ILE* 3.1 45.3 - - + -
98H GLN 5.2 0.2 - - - +
69I LEU* 4.3 21.1 - - + -
97I ILE* 3.8 17.5 - - + -
99I THR* 3.7 11.4 - - - +
67J ASP* 6.1 1.3 - - + -
68J CYS 2.8 9.9 + - - +
69J LEU* 3.4 20.9 - - + -
70J PHE* 3.0 25.5 + - - +
73J VAL* 4.3 4.9 - - - -
95J LYS* 4.5 17.3 - - + +
96J SER* 1.3 81.9 - - - +
98J GLN* 1.3 71.6 + - - +
99J THR* 4.2 2.7 - - - -
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Residues in contact with GLN 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F ARG* 5.7 0.3 + - - -
100F GLU* 3.0 33.0 + - - +
98H GLN 4.7 3.3 - - - +
98I GLN 4.7 2.1 - - - +
99I THR* 2.9 25.1 + - - +
100I GLU* 3.8 18.1 + - + +
70J PHE 3.2 5.8 - - - +
71J ARG 3.4 24.3 + - - +
72J ASP* 3.5 5.9 - - - +
73J VAL* 2.8 45.3 + - + +
74J TRP* 4.9 1.4 - - - -
97J ILE* 1.3 79.0 - - - +
99J THR* 1.3 64.7 + - - +
100J GLU* 6.0 0.2 + - - -
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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