Contacts of the strand formed by residues 39 - 49 (chain B) in PDB entry 2HKN
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 GLY 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLU* 2.8 19.6 - - - +
35A VAL 3.2 10.3 - - - -
36A ILE* 3.7 18.7 - - - +
37B GLY 3.5 3.6 + - - -
38B LYS* 1.3 86.5 - - - +
40B HIS* 1.3 67.2 + - - -
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Residues in contact with HIS 40 (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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34A GLU* 3.1 4.2 + - - -
35A VAL* 2.8 43.5 + - + +
37A GLY* 5.8 1.2 + - - -
38B LYS* 3.5 47.5 + - + -
39B GLY* 1.3 76.6 - - - -
41B ARG* 1.3 63.5 + - - +
42B GLY 3.9 0.3 + - - -
62B LEU* 3.7 22.5 - - + +
64B GLU* 3.4 31.2 + - + -
66B LYS* 3.9 30.3 - - + +
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Residues in contact with ARG 41 (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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32A ARG* 3.7 13.7 - - - +
33A VAL 3.3 4.5 - - - +
34A GLU* 3.1 22.8 + - - +
40B HIS* 1.3 74.7 - - - +
42B GLY* 1.3 59.4 + - - +
62B LEU* 3.6 6.4 - - - +
63B ASP* 3.0 39.7 + - + +
64B GLU 4.7 0.5 + - - -
97B PHE* 3.7 29.9 - - + -
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Residues in contact with GLY 42 (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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32A ARG* 3.4 11.6 + - - +
33A VAL* 2.8 38.0 + - - +
40B HIS 3.9 0.4 + - - -
41B ARG* 1.3 76.8 - - - +
43B THR* 1.3 64.1 + - - -
60B VAL* 4.0 6.1 - - - -
61B ILE 3.2 13.2 - - - -
62B LEU* 4.0 2.2 - - - +
63B ASP* 3.6 8.9 + - - -
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Residues in contact with THR 43 (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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18A MET* 4.5 13.7 - - + -
30A GLY* 3.7 29.4 - - - +
31A SER 3.5 3.4 - - - +
32A ARG* 2.9 29.0 + - - -
42B GLY* 1.3 71.7 - - - -
44B VAL* 1.3 71.6 + - - +
45B ALA* 3.3 1.0 + - - +
60B VAL* 3.7 3.3 - - - +
61B ILE* 2.8 44.9 + - - +
63B ASP* 4.7 0.2 + - - -
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Residues in contact with VAL 44 (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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18A MET* 3.7 5.2 - - - +
27A LEU* 4.0 10.1 - - + -
28A ARG 3.5 24.2 - - - +
29A VAL* 3.8 4.5 - - - -
30A GLY* 2.7 27.9 + - - +
31A SER 3.0 16.8 + - - +
33A VAL* 3.6 28.0 - - + -
43B THR* 1.3 71.5 - - - +
45B ALA* 1.3 60.9 + - - +
46B TYR 4.0 2.0 - - - +
47B VAL* 3.7 27.4 - - + -
58B VAL* 3.8 19.7 - - + -
59B GLY 3.7 5.2 - - - +
60B VAL* 4.4 2.2 - - + +
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Residues in contact with ALA 45 (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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18A MET* 4.1 12.6 - - + -
19A SER* 2.5 31.6 + - - -
29A VAL* 4.1 6.2 - - - +
43B THR 3.3 0.6 + - - +
44B VAL* 1.3 74.6 - - - +
46B TYR* 1.3 60.2 + - - +
59B GLY 2.8 8.7 + - - +
61B ILE* 3.7 22.7 - - + -
79B PHE* 3.5 38.3 - - + +
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Residues in contact with TYR 46 (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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19A SER* 4.6 3.4 - - - -
29A VAL* 4.0 5.2 - - - -
44B VAL* 3.7 1.2 - - - +
45B ALA* 1.3 82.4 - - - +
47B VAL* 1.3 72.4 + - - +
48B GLY* 3.6 24.6 - - - -
49B ALA 2.6 30.6 + - - -
50B THR* 4.1 4.9 - - + -
57B TRP 4.4 2.9 - - - -
58B VAL* 3.4 4.2 - - - +
59B GLY 2.8 32.5 + - - +
78B TYR* 3.6 41.8 - + + +
79B PHE* 3.8 18.2 - - + -
88B PHE* 4.0 15.0 - + - -
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Residues in contact with VAL 47 (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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27A LEU* 4.0 27.4 - - + +
29A VAL* 4.1 13.7 - - + +
44B VAL* 3.7 20.6 - - + -
46B TYR* 1.3 90.0 - - - +
48B GLY* 1.3 61.3 + - - +
56B LYS* 3.4 33.4 - - - +
57B TRP 3.5 7.2 - - - +
58B VAL* 4.4 10.5 - - + -
91B GLN* 5.0 1.1 - - - +
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Residues in contact with GLY 48 (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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46B TYR* 3.6 8.6 - - - -
47B VAL* 1.3 78.7 - - - +
49B ALA* 1.3 66.3 + - - +
56B LYS* 4.3 9.6 - - - +
57B TRP* 2.9 38.0 + - - +
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Residues in contact with ALA 49 (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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46B TYR* 2.6 30.2 + - - -
48B GLY* 1.3 73.3 - - - -
50B THR* 1.3 63.0 + - - +
55B GLY 3.8 14.6 - - - +
56B LYS* 4.8 0.8 - - - +
78B TYR* 4.3 0.7 - - - -
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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