Contacts of the strand formed by residues 18 - 25 (chain A) 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 PHE 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.9 26.9 - - + -
7A GLU 4.3 2.9 - - - -
8A ALA* 4.6 0.2 - - - +
17A LYS* 1.3 72.9 - - - +
19A HIS* 1.3 65.6 + - - +
20A CYS* 3.3 41.1 - - - -
21A GLY* 3.4 7.6 - - - -
34A TYR* 4.4 2.2 - - + -
35A ARG 4.0 10.3 - - - -
36A PRO* 4.1 15.1 - - - +
39A PHE* 3.4 58.3 - + + -
42A TYR* 4.1 16.4 - + + -
69A LEU* 4.5 4.5 - - + -
72A LEU* 4.0 12.1 - - + +
76A GLN* 2.9 26.8 + - - +
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Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLU 2.9 12.3 + - - +
8A ALA* 3.3 26.0 - - - -
9A ASN* 3.4 13.5 - - + +
17A LYS* 3.5 13.2 + - + +
18A PHE* 1.3 76.1 + - - +
20A CYS* 1.3 65.0 + - - +
36A PRO* 3.0 36.1 - - - +
160A TRP 2.6 24.4 + - - -
161A TRP 3.3 24.9 - - - -
162A ASN* 3.8 6.7 - - - -
163A PHE* 3.7 14.8 + - + +
167A MET* 3.4 36.1 - - + +
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Residues in contact with CYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.3 2.6 - - - -
7A GLU* 2.8 45.5 + - - +
18A PHE* 3.3 15.3 - - - -
19A HIS* 1.3 84.2 - - - +
21A GLY* 1.3 59.9 + - - +
34A TYR 3.1 16.8 - - - +
35A ARG* 4.3 0.4 - - - -
163A PHE* 3.9 18.6 - - + -
167A MET* 4.4 1.8 - - - -
168A MET* 3.7 27.6 - - + -
171A ASN* 3.4 16.8 - - - -
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASP 3.3 8.5 - - - -
6A ILE* 4.1 1.1 - - - -
18A PHE* 3.4 12.0 - - - -
20A CYS* 1.3 78.3 - - - +
22A VAL* 1.3 62.6 + - - +
34A TYR* 2.8 36.9 + - - +
42A TYR* 4.2 8.5 - - - -
168A MET* 3.8 0.7 - - - +
171A ASN* 3.1 10.5 - - - -
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A SER* 2.7 36.2 + - - -
5A ASP 3.1 8.5 + - - -
21A GLY* 1.3 80.3 - - - +
23A ILE* 1.3 70.1 + - - +
31A TYR* 4.3 14.8 - - + -
32A VAL 3.4 13.0 - - - +
33A SER* 4.1 3.8 - - - +
42A TYR* 4.2 0.6 - - - -
168A MET* 3.5 21.8 - - + -
171A ASN* 3.5 12.1 - - - +
172A VAL* 3.7 26.0 - - + +
175A VAL* 3.6 28.7 - - + +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ILE* 4.0 23.3 - - + -
3A VAL 3.5 4.0 - - - +
4A SER* 3.7 4.9 - - - +
22A VAL* 1.3 84.5 - - - +
24A TYR* 1.3 73.2 + - - +
25A ASP* 4.5 4.2 - - + +
30A GLU 3.4 2.6 - - - +
31A TYR* 3.3 1.7 - - - -
32A VAL* 2.8 38.8 + - + +
34A TYR* 3.8 17.0 - - + +
42A TYR* 3.6 29.4 - - + -
45A ALA* 3.6 31.2 - - + -
46A LEU* 4.0 12.3 - - + -
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ILE* 3.0 5.9 - - - +
3A VAL* 2.8 42.4 + - + +
23A ILE* 1.3 75.6 - - - +
25A ASP* 1.3 63.6 + - - +
26A TYR* 3.8 37.9 + + - -
29A ALA* 3.5 41.9 - - - +
30A GLU 3.5 7.0 - - - -
31A TYR* 3.3 40.2 - + + +
175A VAL* 3.9 16.4 - - + +
179A LYS* 3.3 35.8 + - + -
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Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 3.6 6.9 + - - +
2A ILE* 3.7 21.5 - - + +
23A ILE* 4.1 5.1 - - + +
24A TYR* 1.3 75.5 - - - +
26A TYR* 1.3 53.8 + - - +
27A SER* 2.8 32.9 + - - -
28A THR* 3.2 19.4 + - + +
29A ALA* 2.7 36.4 + - - -
30A GLU 3.3 9.3 + - - +
49A GLU* 4.8 3.9 - - - +
52A ARG* 4.9 10.6 + - - -
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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