Contacts of the strand formed by residues 29 - 36 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A TRP* 3.9 5.3 - - + -
28A GLN* 1.3 76.9 - - - +
30A ASP* 1.3 62.2 + - - +
31A VAL 3.3 17.9 - - - +
79A THR* 3.3 16.4 - - - +
80A PHE 4.1 5.4 - - - +
81A ALA* 3.9 20.6 - - + -
110A ARG 3.1 5.5 + - - -
111A CYS* 2.9 27.5 - - - -
112A ARG 3.5 0.5 + - - -
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Residues in contact with ASP 30 (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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29A ALA* 1.3 72.7 - - - +
31A VAL* 1.3 61.3 + - - +
77A GLY 3.7 4.7 - - - +
78A VAL* 3.3 24.8 - - + +
79A THR* 2.8 41.6 + - - +
112A ARG* 2.9 39.6 + - - +
113A VAL 2.9 26.0 + - - -
301A PHE* 3.9 9.6 - - + -
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Residues in contact with VAL 31 (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* 6.0 1.8 - - + -
29A ALA* 3.7 3.3 - - - +
30A ASP* 1.3 81.8 - - - +
32A ALA* 1.3 68.4 + - - +
33A ALA* 5.1 0.7 - - + +
78A VAL* 4.0 11.7 - - + -
79A THR 2.9 5.7 + - - +
80A PHE* 3.2 39.3 - - + +
81A ALA 2.9 23.8 + - - -
111A CYS* 4.3 1.8 - - - -
113A VAL 3.4 12.8 - - - +
115A VAL* 3.9 21.5 - - + -
297A LEU* 3.9 9.2 - - + -
301A PHE* 3.5 29.8 - - + -
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Residues in contact with ALA 32 (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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27A TRP* 3.4 37.5 - - + -
31A VAL* 1.3 79.6 - - - +
33A ALA* 1.3 63.7 + - - +
34A LEU* 5.4 0.2 - - - +
81A ALA* 3.3 8.5 - - + +
83A ALA* 5.4 1.1 - - + -
107A VAL* 3.7 9.6 - - + +
111A CYS* 3.7 14.7 - - - -
113A VAL 3.4 5.3 + - - -
114A PRO* 3.4 5.7 - - - +
115A VAL 2.8 24.6 + - - -
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Residues in contact with ALA 33 (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* 3.8 40.6 - - + -
31A VAL* 5.1 1.3 - - + +
32A ALA* 1.3 74.0 - - - +
34A LEU* 1.3 59.8 + - - +
56A ARG* 5.2 0.4 - - - +
81A ALA 2.9 11.9 + - - +
82A ASP* 3.7 8.5 - - - +
83A ALA* 2.8 30.3 + - - +
107A VAL* 5.3 0.2 - - - -
115A VAL* 3.2 14.1 - - + +
117A LEU* 4.7 9.2 - - + -
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Residues in contact with LEU 34 (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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23A PRO* 4.4 7.6 - - + -
33A ALA* 1.3 74.9 - - - +
35A GLY* 1.3 65.8 + - - +
36A VAL* 4.5 4.0 - - + +
56A ARG* 4.5 1.1 - - - -
83A ALA* 4.0 18.8 - - + +
84A GLY 3.4 18.4 - - - +
85A ASP 4.3 1.1 - - - -
86A VAL* 3.9 19.7 - - + +
100A ILE 4.9 0.9 - - - +
103A ALA* 3.8 26.5 - - + +
104A ALA* 3.9 19.5 - - + +
107A VAL* 4.2 13.2 - - + -
115A VAL 2.9 6.1 + - - -
116A PHE* 3.3 27.6 - - + +
117A LEU* 3.0 23.4 + - - -
127A LEU* 5.2 0.7 - - + -
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Residues in contact with GLY 35 (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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34A LEU* 1.3 70.1 - - - +
36A VAL* 1.3 68.5 - - - +
37A PRO* 3.6 5.2 - - - -
52A PRO* 4.3 7.4 - - - -
56A ARG* 3.8 5.1 - - - +
84A GLY 2.9 12.3 + - - -
85A ASP* 3.2 15.5 + - - -
86A VAL* 2.9 28.1 + - - +
117A LEU* 3.5 10.1 - - - -
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Residues in contact with VAL 36 (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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34A LEU* 4.5 7.6 - - + +
35A GLY* 1.3 79.1 - - - +
37A PRO* 1.3 53.4 - - - +
38A PHE* 2.8 21.2 + - + -
52A PRO* 4.0 1.3 - - - +
86A VAL* 4.0 14.1 - - + -
88A LEU* 4.6 4.7 - - + -
100A ILE* 3.4 34.8 - - + -
116A PHE* 5.3 1.1 - - + -
117A LEU 2.8 15.0 + - - +
118A GLY* 3.7 1.9 - - - -
119A GLY* 3.2 19.8 + - - -
123A VAL* 3.5 21.5 - - + -
127A LEU* 4.2 27.8 - - + -
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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