Contacts of the strand formed by residues 22 - 28 (chain B) in PDB entry 1SKW
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 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B GLY* 1.3 70.9 - - - -
23B ILE* 1.3 64.1 + - - +
52B LYS 4.0 15.7 + - - +
53B LEU* 3.5 7.5 - - + -
54B THR* 3.0 24.1 + - - -
80B LEU* 3.9 17.5 - - + -
81B PHE 3.5 7.0 - - - +
82B LYS* 5.1 4.0 - - + +
107B LEU* 4.0 19.7 - - + -
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Residues in contact with ILE 23 (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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5B ILE* 6.0 1.3 - - + -
15B ASP 4.6 5.2 - - - +
16B VAL* 4.5 17.7 - - + +
19B ALA* 4.3 23.8 - - + -
20B ASP 4.7 4.3 - - - +
21B GLY 3.7 13.7 - - - +
22B ALA* 1.3 85.6 - - - +
24B LEU* 1.3 61.1 + - - +
25B VAL* 3.7 11.7 + - + -
54B THR* 3.3 30.5 - - + +
56B ALA* 4.2 21.5 - - + -
79B LEU 3.3 3.1 - - - +
80B LEU* 3.4 3.3 - - - +
81B PHE* 2.7 47.7 + - + +
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Residues in contact with LEU 24 (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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22B ALA 4.3 0.2 - - - -
23B ILE* 1.3 71.1 - - - +
25B VAL* 1.3 59.5 + - - +
26B ASP* 6.1 0.4 - - + -
42B LEU* 4.1 26.0 - - + -
45B ILE* 5.2 0.7 - - + -
53B LEU* 4.2 16.7 - - + +
54B THR 2.8 13.3 + - - +
55B VAL* 3.5 11.3 - - + +
56B ALA 2.7 33.2 + - - +
78B LEU* 4.1 22.0 - - + -
79B LEU 3.4 20.9 - - - +
80B LEU* 4.0 13.2 - - + +
99B LEU* 4.1 12.8 - - + -
102B PHE* 4.4 11.0 - - + -
103B LEU* 4.0 20.4 - - + -
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Residues in contact with VAL 25 (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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7B LEU* 4.0 20.4 - - + -
12B PHE* 4.4 2.9 - - + -
16B VAL* 4.0 23.6 - - + -
23B ILE* 4.2 7.9 - - + -
24B LEU* 1.3 75.8 - - - +
26B ASP* 1.3 65.9 + - - +
27B PHE* 3.7 31.1 + - + -
56B ALA* 3.1 4.7 - - + +
58B LEU* 4.4 4.5 - - + -
77B THR 3.3 1.9 - - - +
78B LEU* 3.3 7.3 - - - -
79B LEU* 2.7 40.3 + - - +
81B PHE* 3.8 28.3 - - + -
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Residues in contact with ASP 26 (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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24B LEU* 4.0 0.9 + - + +
25B VAL* 1.3 73.3 - - - +
27B PHE* 1.3 64.4 + - - +
28B TRP* 3.3 16.5 - - - +
35B CYS 5.5 0.9 - - - +
38B ILE* 4.8 5.7 - - - +
39B ALA* 5.8 1.4 - - - -
42B LEU* 3.5 27.5 - - + +
55B VAL* 5.8 0.2 - - + -
56B ALA 2.7 13.9 + - - +
57B LYS* 3.4 23.6 + - + +
58B LEU 3.0 23.8 + - - -
76B PRO* 3.4 26.4 - - - +
77B THR 3.5 3.1 - - - +
78B LEU* 3.6 12.4 - - + +
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Residues in contact with PHE 27 (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 PHE* 4.2 12.3 - + - -
25B VAL* 3.7 22.0 - - + -
26B ASP* 1.3 70.6 - - - +
28B TRP* 1.3 59.0 + - - +
58B LEU* 3.3 38.4 - - + -
60B ILE* 4.1 18.4 - - + -
66B THR* 4.2 2.2 - - + -
67B ALA* 4.1 20.0 - - + -
70B TYR* 4.2 12.3 - + - -
72B ILE* 4.4 11.2 - - + -
75B ILE* 3.7 8.7 - - + +
76B PRO* 3.4 8.3 - - - +
77B THR* 2.8 53.2 + - + +
79B LEU* 3.5 33.9 - - + -
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Residues in contact with TRP 28 (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 HIS* 6.0 2.2 - - - -
26B ASP* 3.3 34.5 - - - +
27B PHE* 1.3 74.6 - - - +
29B ALA* 1.3 79.4 + - - +
30B GLU* 3.9 18.4 - - + -
35B CYS* 3.6 25.1 - - + +
36B LYS* 6.4 2.5 - - + -
57B LYS* 3.7 35.9 - - + +
58B LEU 3.1 13.4 + - - -
59B ASN* 3.2 45.3 - - + +
60B ILE* 2.9 31.7 + - - +
62B GLN* 5.7 0.9 - - - -
75B ILE* 4.6 2.7 - - - -
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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