Contacts of the strand formed by residues 15 - 22 (chain B) in PDB entry 1WQ9
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 GLN 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B GLN 2.9 25.3 + - - +
11B ARG* 2.7 41.8 + - - +
13B ALA* 3.1 23.4 + - + +
14B CYS* 1.3 79.0 - - - +
16B THR* 1.3 71.6 + - - +
17B ARG* 3.6 11.5 + - - +
45B CYS* 3.4 0.3 - - - -
46B SER* 3.1 28.5 + - - +
91B CYS* 3.4 14.8 - - - -
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Residues in contact with THR 16 (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 ARG* 5.6 0.2 + - - -
15B GLN* 1.3 86.2 - - - +
17B ARG* 1.3 61.0 + - - +
43B LEU* 4.0 26.7 - - + +
44B ARG 3.5 5.4 - - - -
45B CYS* 4.1 1.8 - - - -
88B HIS* 3.5 26.2 - - + +
89B THR 3.6 21.8 + - - +
90B ALA* 4.6 0.4 - - - -
91B CYS* 3.4 20.6 - - - -
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Residues in contact with ARG 17 (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 GLU* 2.8 47.5 + - - +
19A THR* 6.5 0.2 - - - +
20A LEU* 3.7 19.8 - - - +
11B ARG* 2.9 41.2 + - - +
12B SER 3.9 0.2 + - - -
13B ALA 3.0 14.6 + - - -
15B GLN* 3.6 6.8 + - + +
16B THR* 1.3 76.7 - - - +
18B GLU* 1.3 68.8 + - - +
19B THR* 2.8 21.8 + - - +
43B LEU* 3.4 8.9 - - - -
44B ARG 2.9 21.1 + - - +
46B SER* 2.7 49.0 + - - +
47B GLY* 3.7 5.3 - - - -
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Residues in contact with GLU 18 (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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11A ARG* 2.8 54.5 + - - +
17A ARG* 3.1 31.6 + - - +
18A GLU 5.4 3.6 - - - +
17B ARG* 1.3 79.3 - - - +
19B THR* 1.3 64.1 + - - +
20B LEU* 5.7 0.7 - - + -
41B ALA* 3.7 20.4 - - + +
42B VAL 3.8 5.8 - - - -
43B LEU* 3.9 8.9 - - + +
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Residues in contact with THR 19 (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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17B ARG* 2.8 19.1 + - - +
18B GLU* 1.3 76.2 + - - +
20B LEU* 1.3 75.6 + - - +
21B VAL* 3.6 3.9 + - + -
40B VAL 3.5 0.7 - - - +
41B ALA* 3.4 2.5 - - - -
42B VAL* 2.8 44.1 + - - +
44B ARG* 3.4 30.4 + - + +
46B SER* 5.0 2.6 + - - -
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Residues in contact with LEU 20 (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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11A ARG 4.1 6.7 - - - +
12A SER* 4.2 3.6 - - - -
17A ARG* 3.7 35.7 - - - +
46A SER* 4.0 7.6 - - - +
47A GLY* 3.6 36.8 - - - +
18B GLU* 5.7 0.7 - - + -
19B THR* 1.3 80.4 - - - +
21B VAL* 1.3 64.3 + - - +
39B CYS* 4.1 20.9 - - + -
40B VAL 3.4 9.4 - - - +
41B ALA* 4.1 13.9 - - + -
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Residues in contact with VAL 21 (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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19B THR* 4.0 13.5 - - + +
20B LEU* 1.3 80.7 - - - +
22B SER* 1.3 60.3 + - - +
23B ILE 3.7 0.2 + - - -
26B GLU* 3.5 31.2 - - + +
39B CYS* 3.2 6.7 - - - -
40B VAL* 2.9 55.7 + - + +
42B VAL* 4.1 10.3 - - + -
44B ARG* 3.8 30.3 - - - +
85B PHE* 4.5 4.0 - - + -
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Residues in contact with SER 22 (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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21B VAL* 1.3 72.1 - - - +
23B ILE* 1.3 60.0 + - - +
24B LEU* 3.6 4.9 + - - +
25B GLN* 2.7 45.6 + - - +
26B GLU* 2.9 31.7 + - - +
38B SER* 3.7 10.6 + - - -
39B CYS* 4.2 4.3 - - - +
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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