Contacts of the strand formed by residues 92 - 100 (chain J) in PDB entry 4KRM
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 92 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38J ARG* 3.9 15.5 - - + -
39J GLN 3.3 32.5 - - - +
40J ALA* 3.5 6.7 - - + +
41J PRO* 4.9 2.7 - - - -
90J ASP 3.2 7.3 + - - +
91J THR* 1.3 77.6 - - - +
93J ILE* 1.3 63.1 + - - +
94J TYR* 3.4 6.8 - - + -
119J GLN* 3.5 10.5 - - - +
120J VAL 2.9 31.0 + - - +
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Residues in contact with ILE 93 (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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38J ARG* 3.1 4.7 - - - -
39J GLN* 2.9 35.9 + - + +
92J ALA* 1.3 72.9 - - - +
94J TYR* 1.3 63.2 + - - +
95J TYR* 3.5 37.5 - - + +
116J GLN 4.6 1.6 - - - +
117J GLY* 3.9 6.5 - - - -
118J THR 3.8 23.8 - - - +
119J GLN* 3.2 26.4 - - + +
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Residues in contact with TYR 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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6J GLU* 3.8 6.9 - - - +
20J LEU* 3.6 30.3 - - + -
36J TRP* 4.1 5.1 - + + -
37J PHE 3.3 7.0 - - - -
38J ARG* 2.9 44.5 + - + -
48J VAL* 4.2 12.1 - - + -
68J PHE* 4.4 3.8 - + - -
81J LEU* 4.6 7.0 - - + -
83J MET* 3.3 25.7 - - + +
90J ASP* 2.6 32.0 + - - +
92J ALA* 3.4 11.9 - - + -
93J ILE* 1.3 75.0 - - - +
95J TYR* 1.3 62.2 + - - +
117J GLY* 3.3 2.8 - - - -
118J THR* 3.0 33.2 + - + +
120J VAL* 3.3 28.5 - - + -
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Residues in contact with TYR 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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6J GLU* 3.4 1.8 - - - +
35J GLY 3.8 0.2 - - - +
36J TRP* 3.4 9.4 - - - -
37J PHE* 2.6 43.4 + - + +
39J GLN* 3.9 25.6 + - + +
45J ARG* 3.8 40.8 + - + -
93J ILE* 3.5 43.8 - - + +
94J TYR* 1.3 72.3 - - - +
96J CYS* 1.3 61.1 + - - +
114J TRP* 4.0 20.9 - - + -
115J GLY 3.9 11.0 - - - -
116J GLN 3.2 25.8 + - - -
117J GLY* 3.7 13.5 - - - -
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Residues in contact with CYS 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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4J LEU* 4.0 7.6 - - + -
6J GLU* 2.8 26.1 + - + +
22J CYS* 2.0 51.6 - - + -
34J MET* 3.8 18.2 - - - -
35J GLY 3.6 6.7 - - - -
36J TRP* 4.2 7.4 - - + -
79J VAL* 4.0 4.7 - - - -
95J TYR* 1.3 74.3 - - - +
97J ALA* 1.3 64.3 + - - +
114J TRP* 3.6 4.5 - - - -
115J GLY 3.0 24.3 + - - -
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Residues in contact with ALA 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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4J LEU* 3.9 5.2 - - - -
34J MET* 3.3 10.4 - - - +
35J GLY 2.8 33.8 + - - +
37J PHE* 4.0 5.4 - - + -
96J CYS* 1.3 77.9 - - - +
98J ALA* 1.3 61.1 + - - +
111J TYR* 3.4 25.6 - - + -
113J TYR 3.3 11.0 - - - +
114J TRP* 3.9 22.2 - - + -
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Residues in contact with ALA 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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2J VAL* 4.7 3.8 - - + -
4J LEU* 3.9 13.7 - - + +
32J TYR* 3.7 19.5 - - + -
33J GLY 3.5 4.5 - - - -
34J MET* 3.7 21.8 - - + -
97J ALA* 1.3 74.6 - - - +
99J ALA* 1.3 60.0 + - - +
100J ALA 4.1 0.2 - - - -
111J TYR* 3.6 3.1 - - - -
112J ASP* 2.8 26.3 + - - +
113J TYR* 3.0 20.4 + - + +
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Residues in contact with ALA 99 (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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353I ARG* 4.1 3.6 - - - +
32J TYR* 3.4 3.1 - - - -
33J GLY* 2.8 41.2 + - - +
98J ALA* 1.3 74.0 - - - +
100J ALA* 1.3 65.4 + - - +
101J GLY* 3.6 1.2 - - - +
103J ALA 4.4 2.6 - - - +
105J TYR* 4.1 21.8 - - + -
110J GLU 3.6 20.4 - - - +
111J TYR* 3.7 14.1 - - + -
112J ASP* 3.5 4.9 - - - -
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Residues in contact with ALA 100 (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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325I LEU* 3.9 11.9 - - + -
350I VAL* 3.5 22.6 - - + +
353I ARG* 3.0 23.2 + - - -
355I ASP* 3.8 7.3 - - - +
30J ARG* 3.5 21.5 - - - +
31J SER 3.6 0.7 - - - -
32J TYR* 3.5 25.4 - - + -
99J ALA* 1.3 68.9 - - - +
101J GLY* 1.3 57.1 + - - +
105J TYR* 5.8 0.9 - - - -
112J ASP* 3.0 9.5 + - - +
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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