Contacts of the strand formed by residues 7 - 15 (chain B) in PDB entry 5SZK
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 TYR 7 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668A GLU* 5.0 1.6 - - - -
671A ARG* 4.6 3.1 - - - +
5B TYR* 3.3 10.5 - - - -
6B ASP* 1.3 86.9 - - + +
8B LEU* 1.3 53.8 + - - +
9B PHE* 3.8 24.7 - + + -
55B LYS* 3.1 47.4 + - + -
56B THR 3.3 2.8 + - - -
57B ILE* 3.3 27.0 - - + +
58B LYS 2.8 30.8 + - - -
170B LYS* 4.5 22.6 - - + +
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Residues in contact with LEU 8 (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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664A VAL* 4.1 26.2 - - + +
665A ASP* 4.7 4.5 - - - +
668A GLU* 3.3 42.6 + - + +
5B TYR* 3.8 6.7 - - + +
7B TYR* 1.3 72.2 - - - +
9B PHE* 1.3 75.2 + - - +
10B LYS* 4.1 22.2 - - + +
58B LYS* 3.3 39.3 - - + +
60B GLN* 4.4 10.3 - - + -
82B HIS* 3.7 13.2 - - - -
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Residues in contact with PHE 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 3.8 34.1 - + + -
8B LEU* 1.3 85.6 - - - +
10B LYS* 1.3 63.1 + - - +
11B LEU* 3.8 15.8 + - + +
52B LEU* 6.1 0.7 - - + -
57B ILE* 3.9 25.6 - - + -
58B LYS 2.9 8.5 + - - -
59B LEU* 3.4 17.6 - - + -
60B GLN* 2.9 25.3 + - - +
82B HIS* 3.6 7.2 - + - -
166B ALA* 3.9 24.2 - - + -
169B ILE* 4.0 35.9 - - + -
170B LYS* 4.3 16.8 - - + -
173B MET* 5.6 7.2 - - + -
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Residues in contact with LYS 10 (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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661A ASP* 3.6 12.5 + - - -
664A VAL* 4.9 0.8 - - - +
665A ASP* 2.7 31.6 + - - -
8B LEU* 4.1 18.5 - - + +
9B PHE* 1.3 73.4 - - - +
11B LEU* 1.3 67.5 + - - +
60B GLN* 3.2 33.2 + - + +
62B TRP* 4.4 12.6 - - + +
80B GLY 3.9 25.1 - - - +
81B ALA* 4.0 6.2 - - + -
82B HIS* 3.0 41.3 + - + +
83B GLY 3.2 3.6 + - - +
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Residues in contact with LEU 11 (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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9B PHE* 4.0 16.2 - - + +
10B LYS* 1.3 84.0 - - - +
12B LEU* 1.3 59.8 + - - +
59B LEU* 4.4 13.7 - - + -
60B GLN 2.7 7.4 + - - +
61B ILE* 3.4 36.8 - - + -
62B TRP* 2.7 36.6 + - - +
81B ALA* 4.9 1.8 - - - -
83B GLY 3.2 7.6 - - - +
85B ILE* 5.0 3.6 - - + -
162B PHE* 4.2 17.0 - - + +
165B MET* 4.1 26.0 - - + -
166B ALA 5.6 1.1 - - - +
169B ILE* 3.7 24.7 - - + -
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Residues in contact with LEU 12 (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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11B LEU* 1.3 76.4 - - - +
13B LEU* 1.3 60.2 + - - +
14B ILE* 4.0 17.0 - - + -
62B TRP* 3.4 29.2 - - + -
64B THR* 4.0 15.9 - - + -
77B TYR* 3.8 21.1 - - + +
78B TYR* 3.7 46.4 - - + -
81B ALA* 4.5 4.5 - - + -
83B GLY 2.8 11.8 + - - +
84B ILE* 3.9 16.4 - - + -
85B ILE* 2.8 35.3 + - - +
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Residues in contact with LEU 13 (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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11B LEU* 6.3 0.2 - - + -
12B LEU* 1.3 74.0 - - - +
14B ILE* 1.3 58.2 + - - +
21B LYS* 3.7 37.3 - - + +
24B LEU* 5.3 5.8 - - + -
25B LEU* 4.0 14.1 - - + +
61B ILE* 3.7 26.9 - - + -
62B TRP 2.9 13.2 + - - +
63B ASP* 4.7 7.0 - - - -
64B THR* 2.7 34.5 + - - +
85B ILE* 3.6 39.3 - - + -
87B VAL* 4.1 11.2 - - + -
162B PHE* 4.3 12.8 - - + -
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Residues in contact with ILE 14 (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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12B LEU* 4.0 10.5 - - + -
13B LEU* 1.3 80.4 - - - +
15B GLY* 1.3 59.9 + - - +
21B LYS* 3.4 11.3 - - - +
64B THR* 3.7 11.0 - - + +
78B TYR* 3.6 35.7 - - + +
84B ILE* 3.9 25.4 - - + -
85B ILE 3.0 14.7 + - - +
86B VAL* 3.9 8.1 - - + -
87B VAL* 2.9 25.6 + - - +
102B TRP* 3.9 25.4 - - + +
106B ILE* 3.9 22.9 - - + -
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Residues in contact with GLY 15 (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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14B ILE* 1.3 79.1 - - - +
16B ASP* 1.3 69.0 + - - -
19B VAL* 4.6 0.2 - - - -
21B LYS* 3.0 14.8 + - - +
64B THR* 4.9 0.2 + - - -
66B GLY* 3.4 13.2 - - - -
87B VAL 3.5 15.5 - - - -
102B TRP* 3.4 28.0 - - - -
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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