Contacts of the strand formed by residues 29 - 35 (chain B) in PDB entry 1WOH
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 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B TRP* 4.3 3.8 - - + -
28B GLN* 1.3 77.8 - - - +
30B ASP* 1.3 63.0 + - - +
31B VAL 4.0 10.5 - - - +
79B THR* 3.4 24.7 - - - +
80B PHE 4.3 1.8 - - - +
81B ALA* 4.0 20.2 - - + -
110B ARG 3.0 6.5 + - - -
111B CYS* 2.8 27.9 - - - -
112B ARG 3.3 1.0 + - - -
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Residues in contact with ASP 30 (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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29B ALA* 1.3 70.3 - - - +
31B VAL* 1.3 61.5 + - - +
77B GLY 3.7 4.7 - - - +
78B VAL* 3.3 25.0 - - + -
79B THR* 2.7 40.7 + - - +
111B CYS* 3.9 0.2 - - - +
112B ARG* 3.0 40.2 + - - +
113B VAL* 2.9 27.2 + - - +
301B PHE* 3.9 8.6 - - + -
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Residues in contact with VAL 31 (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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15B PHE* 5.9 2.2 - - + -
29B ALA* 4.0 2.9 - - - +
30B ASP* 1.3 76.2 - - - +
32B ALA* 1.3 65.6 + - - +
33B ALA 5.2 0.2 - - - +
78B VAL* 3.9 13.5 - - + -
79B THR 2.9 5.8 + - - +
80B PHE* 3.1 34.0 - - + +
81B ALA* 2.9 24.3 + - - -
111B CYS* 4.4 0.7 - - - -
113B VAL 3.4 13.2 - - - +
115B VAL* 3.8 21.1 - - + -
297B LEU* 3.9 13.9 - - + -
301B PHE* 3.5 35.2 - - + -
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Residues in contact with ALA 32 (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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27B TRP* 3.6 18.4 - - + -
31B VAL* 1.3 80.3 - - - +
33B ALA* 1.3 55.9 + - - +
34B LEU* 5.4 0.2 - - - +
81B ALA* 3.4 7.6 - - + +
83B ALA* 5.8 0.9 - - + -
107B VAL* 3.5 26.5 - - + +
111B CYS* 3.6 18.8 - - + -
113B VAL 3.4 5.1 + - - -
114B PRO* 3.3 4.3 - - - +
115B VAL 2.7 31.5 + - - -
116B PHE* 6.0 0.2 - - - -
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Residues in contact with ALA 33 (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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15B PHE* 3.8 40.6 - - + -
31B VAL* 5.2 1.1 - - + +
32B ALA* 1.3 73.4 - - - +
34B LEU* 1.3 62.7 + - - +
56B ARG* 5.2 0.2 - - - -
81B ALA 2.9 13.6 + - - +
82B ASP* 3.7 7.8 - - - +
83B ALA* 2.9 30.5 + - - +
107B VAL* 5.3 0.2 - - - -
115B VAL* 3.2 12.1 - - + +
117B LEU* 4.8 8.7 - - + -
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Residues in contact with LEU 34 (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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23B PRO* 4.5 3.8 - - + -
33B ALA* 1.3 76.1 - - - +
35B GLY* 1.3 70.5 + - - +
36B VAL* 4.4 4.1 - - + +
56B ARG* 4.5 0.4 - - - -
83B ALA* 4.2 18.2 - - + +
84B GLY 3.5 16.6 - - - +
85B ASP 4.3 0.4 - - - -
86B VAL* 4.1 19.5 - - + +
100B ILE 4.9 0.7 - - - +
103B ALA* 3.9 28.5 - - + +
104B ALA* 4.0 9.4 - - + +
107B VAL* 4.2 13.7 - - + -
115B VAL 2.8 8.1 + - - +
116B PHE* 3.3 38.8 - - + -
117B LEU* 2.9 24.5 + - - +
127B LEU* 5.2 0.9 - - + -
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Residues in contact with GLY 35 (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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34B LEU* 1.3 72.2 - - - +
36B VAL* 1.3 66.7 + - - +
37B PRO* 3.6 1.1 - - - -
52B PRO* 4.2 3.1 - - - -
56B ARG* 3.7 5.4 - - - +
84B GLY 2.9 11.7 + - - -
85B ASP* 3.0 20.0 + - - -
86B VAL* 3.0 27.9 + - - +
117B LEU* 3.4 14.1 - - - -
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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