Contacts of the strand formed by residues 34 - 39 (chain B) in PDB entry 4LKC
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.8 28.3 - - + -
27B PHE* 4.7 1.8 - - - -
29B PHE* 3.8 34.8 - - + -
32B TYR* 3.9 13.7 - - - +
33B ASP* 1.3 77.3 - - - +
35B HIS* 1.4 66.7 + - - +
50B ALA* 3.4 2.9 - - - +
51B ILE* 2.8 39.6 + - + +
69B ILE* 4.0 0.6 - - - +
71B ARG* 4.2 4.3 - - - +
78B LEU* 3.7 22.2 - - + -
95B CYS* 3.8 16.8 - - - -
96B VAL 3.5 19.3 - - - +
97B ARG* 3.7 24.5 - - - -
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Residues in contact with HIS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.7 0.4 - - - -
97A ILE* 3.3 27.7 - - + +
33B ASP* 5.0 1.5 - - + +
34B MET* 1.4 77.0 + - - +
36B TRP* 1.3 67.3 + - - +
37B VAL* 4.2 3.8 - - + -
47B TRP* 3.1 24.4 + - + +
49B SER 3.2 7.4 - - - +
50B ALA* 3.5 20.1 - - + +
69B ILE* 4.4 1.1 - - - -
78B LEU* 3.8 6.2 - - - +
95B CYS* 3.7 3.1 - - - -
96B VAL* 2.8 50.6 + - + +
97B ARG 4.8 0.2 - - - -
98B GLU* 2.8 44.8 + - + +
115B MET* 4.2 15.5 - - + +
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Residues in contact with TRP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 4.0 10.8 - - + -
20B LEU* 3.9 23.8 - - + -
21B SER 3.7 22.4 - - - -
22B CYS* 3.8 13.2 - - + -
35B HIS* 1.3 71.2 - - - +
37B VAL* 1.3 64.0 + - - +
47B TRP* 4.0 1.0 - - - -
48B VAL* 2.9 34.2 + - + +
49B SER* 3.1 22.8 + - - +
69B ILE* 3.5 29.6 - - + -
78B LEU* 3.5 36.9 - - + +
79B TYR 3.1 25.0 + - - -
80B LEU* 3.6 23.3 - - + -
93B TYR* 4.4 14.1 - - + -
94B TYR 3.2 26.0 - - - -
95B CYS 3.9 12.1 - - - -
122B THR* 4.9 0.2 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 4.0 16.2 - - + -
35B HIS* 4.5 2.2 - - + -
36B TRP* 1.3 79.5 - - - +
38B ARG* 1.3 61.9 + - - +
45B LEU* 4.2 7.2 - - + -
46B GLU 3.4 18.2 - - - +
47B TRP* 4.3 11.7 - - + -
48B VAL* 3.8 1.8 - - - -
93B TYR* 3.7 1.1 - - - -
94B TYR* 2.8 36.7 + - + +
96B VAL* 3.9 16.2 - - + -
115B MET* 4.1 24.9 - - + -
118B TRP* 3.7 29.8 - - + -
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 1.3 74.2 - - - +
39B GLN* 1.3 64.5 + - - +
40B ALA 5.6 0.2 - - - +
44B GLY 3.9 0.2 - - - +
45B LEU* 3.6 1.4 - - - -
46B GLU* 2.7 85.2 + - + +
48B VAL* 3.5 16.4 - - + +
62B SER* 4.1 9.9 + - - -
63B VAL* 3.8 24.4 - - - +
67B PHE* 3.9 2.0 - - - -
88B GLY 3.8 16.5 + - - -
89B ASP* 2.8 31.6 + - - +
91B ALA* 3.9 12.1 - - + -
92B VAL 3.3 10.1 - - - +
93B TYR* 3.0 39.3 + - + -
94B TYR* 5.2 0.9 - - - -
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 2.8 43.0 + - - -
88A TYR* 3.3 11.5 + - - -
38B ARG* 1.3 76.6 - - - +
40B ALA* 1.3 65.9 + - - +
41B THR* 3.9 0.9 + - - +
42B GLY 5.8 0.2 - - - +
43B LYS 3.0 28.7 + - - +
44B GLY 3.6 10.1 - - - +
45B LEU* 3.9 16.8 - - + +
91B ALA* 3.6 2.9 - - - -
92B VAL* 3.0 34.3 + - + +
94B TYR* 4.0 14.1 + - + -
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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