Contacts of the strand formed by residues 34 - 39 (chain J) in PDB entry 3KYM
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 MET 34 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4J LEU* 4.1 22.0 - - + -
22J CYS* 4.6 6.1 - - - -
27J PHE* 4.9 2.7 - - - -
29J PHE* 3.7 36.6 - - + -
32J TYR* 4.0 7.6 - - - +
33J PRO* 1.3 82.0 - - - +
35J PHE* 1.3 62.4 + - - +
50J TRP* 3.5 6.8 - - - -
51J ILE* 2.9 33.9 + - + +
70J ILE* 4.5 0.9 - - - +
72J ARG* 3.9 8.3 - - - +
79J LEU* 3.7 33.0 - - + -
97J ALA 3.6 21.5 - - - +
98J ARG* 3.8 23.3 - - - +
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Residues in contact with PHE 35 (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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94I TRP* 4.3 4.3 - + - -
96I LEU* 3.9 12.8 - - + -
34J MET* 1.3 75.4 - - - +
36J TRP* 1.3 69.2 - - - +
37J VAL* 4.6 2.7 - - + -
47J TRP* 3.3 34.3 - + - -
49J SER 3.3 6.1 - - - -
50J TRP* 3.3 28.0 - + + -
79J LEU* 3.8 3.7 - - - +
96J CYS* 3.3 7.1 - - - +
97J ALA* 2.7 42.7 + - + +
98J ARG 4.2 0.2 - - - -
99J GLU* 3.4 44.0 - - + -
104J TRP 4.1 5.8 - - - -
105J TYR 4.2 1.3 - - - -
106J PHE* 3.4 37.7 - + + -
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Residues in contact with TRP 36 (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* 3.7 9.2 - - + -
20J LEU* 4.1 30.5 - - + -
21J SER 4.1 4.9 - - - -
22J CYS* 3.7 16.4 - - + -
35J PHE* 1.3 73.9 - - - +
37J VAL* 1.3 62.7 + - - +
47J TRP* 4.6 0.8 - - - -
48J VAL* 3.0 33.5 + - + +
49J SER* 3.4 20.4 + - - +
70J ILE* 3.7 25.6 - - + -
79J LEU* 3.2 44.4 - - + +
80J TYR 3.4 10.9 + - - -
81J LEU* 4.0 30.3 - - + -
94J TYR* 4.5 12.6 - - + -
95J TYR 3.5 23.6 - - - -
96J CYS* 3.5 23.1 - - + -
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Residues in contact with VAL 37 (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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98I PHE* 4.0 15.3 - - + -
35J PHE* 4.6 4.5 - - + -
36J TRP* 1.3 78.8 - - - +
38J ARG* 1.3 72.2 + - - +
45J LEU* 4.5 5.4 - - + -
46J GLU 3.5 23.1 - - - +
47J TRP* 3.8 6.3 - - + +
48J VAL* 4.5 0.7 - - - -
94J TYR* 3.4 5.1 - - - +
95J TYR* 2.6 45.1 + - + +
97J ALA* 4.6 9.6 - - + -
106J PHE* 3.8 28.9 - - + -
109J TRP* 4.1 23.3 - - + -
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Residues in contact with ARG 38 (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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37J VAL* 1.3 79.8 - - - +
39J GLN* 1.3 62.0 + - - +
40J ALA 5.7 0.4 - - - +
45J LEU* 3.5 4.4 - - - +
46J GLU* 2.7 73.3 + - + +
48J VAL* 3.5 12.0 - - + +
63J SER* 3.1 23.8 + - - -
64J VAL* 4.5 7.0 - - - +
67J ARG* 5.6 0.2 - - - +
68J PHE* 4.6 4.0 - - - -
89J GLU* 4.2 12.8 + - - +
90J ASP* 2.7 34.8 + - - +
92J ALA* 4.4 9.4 - - + -
93J THR 3.2 12.6 - - - +
94J TYR* 2.8 50.4 + - + -
95J TYR* 4.5 2.5 - - - +
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Residues in contact with GLN 39 (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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38I GLN* 2.8 42.8 + - - -
87I TYR* 3.4 10.5 + - - -
38J ARG* 1.3 79.0 - - - +
40J ALA* 1.3 66.9 + - - +
41J PRO* 3.9 0.7 - - - +
42J GLY 5.7 0.7 - - - +
43J LYS 3.1 22.6 + - - +
44J GLY 3.4 14.1 + - - +
45J LEU* 3.7 18.2 - - + +
46J GLU* 6.1 0.2 - - - -
92J ALA* 3.6 2.9 - - - -
93J THR* 2.9 37.7 + - - +
95J TYR* 3.6 13.9 + - + -
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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