Contacts of the strand formed by residues 93 - 98 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16K THR 3.4 14.1 - - - +
19K VAL* 3.5 7.4 - - + +
26K TYR* 3.6 21.3 - - + +
27K LEU 3.7 4.9 - - - +
28K ASN* 3.5 22.4 - - - +
64L VAL 3.0 16.3 + - - +
65L GLN* 3.1 7.3 - - + +
66L MSE 2.9 23.2 + - - -
92L PRO* 1.3 74.6 - - - +
94L ARG* 1.3 62.1 + - - +
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Residues in contact with ARG 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K ARG* 3.2 13.5 + - - +
14K GLY 3.1 28.1 + - - -
15K HIS* 3.8 17.0 - - + +
27K LEU 4.9 0.4 + - - -
28K ASN* 2.8 24.0 + - - +
29K TYR* 2.8 37.5 + - + -
115K ASP* 4.9 0.9 - - - -
65L GLN* 4.3 4.5 - - - +
66L MSE 3.2 25.1 - - + +
68L CYS* 4.3 7.0 - - - -
76L ILE* 4.3 5.5 - - - +
79L MSE 3.6 29.9 - - - +
80L GLU* 2.7 35.4 + - - +
83L ILE* 3.6 18.1 - - - +
92L PRO* 4.6 3.4 - - - +
93L ALA* 1.3 78.0 - - - +
95L LYS* 1.3 63.2 + - - +
96L SER* 4.5 5.2 + - - -
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Residues in contact with LYS 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G LYS* 5.8 2.0 - - - +
29K TYR* 4.1 21.3 - - + -
67K ASP* 2.6 37.3 + - + +
69K LEU* 3.9 29.4 - - + -
95K LYS* 5.7 1.1 - - - +
97K ILE* 5.4 5.2 - - - -
115K ASP* 2.9 32.2 + - + +
65L GLN* 4.4 1.0 - - - +
66L MSE 3.2 3.8 + - - +
67L ASP* 3.0 36.5 + - - +
68L CYS* 2.9 25.5 + - - +
94L ARG* 1.3 78.1 - - - +
96L SER* 1.3 62.2 + - - +
97L ILE* 4.2 15.2 - - + +
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Residues in contact with SER 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K TYR* 5.2 3.3 - - - -
69K LEU* 3.9 12.5 - - - +
99K THR* 4.8 1.9 + - - +
100K GLU 5.3 1.2 - - - +
101K PHE* 5.6 2.6 - - - -
113K GLN* 4.7 4.6 + - - +
68L CYS* 3.3 11.9 - - - +
70L PHE* 3.5 22.0 - - - -
73L VAL* 4.3 5.5 - - - +
76L ILE* 3.5 33.4 - - - +
79L MSE 3.9 7.6 - - - +
94L ARG* 4.5 4.9 + - - -
95L LYS* 1.3 74.8 - - - +
97L ILE* 1.3 67.4 + - - +
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Residues in contact with ILE 97 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95G LYS* 6.5 0.2 - - - -
97G ILE* 3.4 40.8 - - + -
98G GLN 5.1 0.4 - - - +
69K LEU* 4.3 12.6 - - + -
97K ILE* 4.3 14.6 - - + -
99K THR* 3.7 11.9 - - - +
67L ASP* 6.1 1.3 - - + -
68L CYS 2.9 8.2 + - - +
69L LEU* 3.6 20.9 - - + -
70L PHE* 2.9 25.8 + - - +
73L VAL* 4.4 5.2 - - - -
95L LYS* 4.2 26.5 - - + -
96L SER* 1.3 82.1 - - - +
98L GLN* 1.3 76.6 + - - +
99L THR* 3.8 7.9 - - + -
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Residues in contact with GLN 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ARG* 5.7 0.3 + - - -
100C GLU* 3.0 28.4 + - - +
98G GLN 4.7 3.1 - - - +
98K GLN 4.7 2.6 - - - +
99K THR* 2.9 23.1 + - - +
100K GLU* 3.6 23.6 - - - +
70L PHE 3.2 5.6 - - - +
71L ARG 3.4 25.8 + - - +
72L ASP* 3.7 6.1 - - - +
73L VAL* 3.0 41.8 + - + +
74L TRP* 4.9 1.4 - - - -
97L ILE* 1.3 80.1 - - - +
99L THR* 1.3 63.4 + - - +
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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