Contacts of the strand formed by residues 15 - 21 (chain A) in PDB entry 1OWK
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 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.9 15.1 - - + +
12A GLN* 3.1 26.1 + - + +
13A PRO 3.4 2.1 - - - +
14A TRP* 1.3 82.8 - - + +
16A ALA* 1.3 79.0 + - - +
17A ALA* 4.1 3.9 + - + -
28A TYR* 3.5 22.0 - - - -
31A GLY* 4.0 12.8 - - - -
32A GLY 3.7 3.1 - - - -
59A TYR 4.2 2.1 - - - +
60A LEU* 4.0 12.0 - - - +
61A GLY 4.7 0.3 + - - -
62A ARG 5.2 2.9 - - - -
137A THR* 3.6 27.1 - - - -
138A GLY* 4.1 4.9 - - - -
139A PHE* 3.6 27.4 - + - -
153A LEU* 3.8 24.2 - - + -
200A PRO* 3.9 20.9 - - + -
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Residues in contact with ALA 16 (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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14A TRP 3.6 1.7 + - - +
15A PHE* 1.3 80.7 - - - +
17A ALA* 1.3 60.1 + - - +
18A ILE* 4.7 1.8 - - + -
31A GLY* 3.4 9.2 - - - -
32A GLY* 3.0 43.5 + - - +
33A SER* 4.5 1.3 - - - +
40A VAL* 4.4 11.0 - - + -
58A VAL* 4.0 15.9 - - + -
59A TYR 3.5 5.2 - - - +
60A LEU* 3.7 17.9 - - + -
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Residues in contact with ALA 17 (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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15A PHE* 4.1 6.1 + - + -
16A ALA* 1.3 69.6 - - - +
18A ILE* 1.3 62.0 + - - +
19A TYR* 3.5 27.2 - - + +
28A TYR* 4.0 14.6 - - + -
58A VAL* 3.5 2.1 - - - -
59A TYR* 2.9 47.3 + - + +
62A ARG* 4.6 7.6 - - + +
139A PHE* 4.2 15.3 - - + -
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Residues in contact with ILE 18 (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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16A ALA* 4.3 7.4 - - + +
17A ALA* 1.3 76.0 - - - +
19A TYR* 1.3 68.5 + - - +
28A TYR* 3.9 4.8 - - - -
29A VAL* 2.9 27.8 + - + +
30A CYS* 2.9 25.3 + - - +
31A GLY 3.9 17.9 - - - +
40A VAL* 4.6 7.6 - - + -
42A SER* 4.3 7.2 - - - +
47A PHE* 3.8 31.6 - - + -
56A TYR* 4.2 6.7 - - + -
57A ILE 3.4 7.6 - - - +
58A VAL* 4.1 19.3 - - + -
100A LEU* 3.7 25.1 - - + -
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Residues in contact with TYR 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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17A ALA* 3.5 33.9 - - + +
18A ILE* 1.3 76.1 - - - +
20A ARG* 1.3 63.0 + - - +
26A VAL* 3.7 22.9 - - + -
27A THR 3.5 20.0 - - - +
28A TYR* 3.8 23.6 - + + -
29A VAL* 4.0 2.9 - - - -
56A TYR* 3.3 12.5 - - - -
57A ILE* 2.7 40.4 + - + +
59A TYR* 3.9 22.9 - + - -
62A ARG* 3.1 26.8 + - - -
64A ARG 4.3 0.2 + - - -
65A LEU* 3.2 31.2 + - + +
139A PHE* 5.0 0.9 - - - -
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Residues in contact with ARG 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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19A TYR* 1.3 80.5 - - - +
21A ARG* 1.3 71.1 + - - +
22A HIS* 3.2 46.6 + - - -
23A ARG* 3.2 25.7 - - - +
26A VAL* 3.5 5.2 - - - +
27A THR* 3.1 21.4 + - - +
29A VAL* 3.6 20.4 - - + +
50A TYR* 3.2 55.4 + - - +
55A ASP* 3.1 19.3 + - + +
56A TYR* 3.9 26.2 - - + -
57A ILE* 4.8 0.7 - - - +
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Residues in contact with ARG 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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20A ARG* 1.3 86.3 + - - +
22A HIS* 1.3 64.5 + - - +
23A ARG* 5.8 0.2 - - - -
24A GLY* 5.7 1.6 - - - +
25A SER 3.7 5.4 - - - +
26A VAL* 4.0 9.6 - - + -
54A GLU 2.9 27.9 + - - -
55A ASP* 3.0 21.1 + - - +
56A TYR 3.8 12.3 + - - -
57A ILE* 3.7 34.4 - - + +
74A LYS* 5.3 7.3 - - - +
76A GLU* 3.7 24.7 + - - +
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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