Contacts of the strand formed by residues 80 - 85 (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 PHE 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PHE* 5.0 7.6 - + - -
16A ALA* 4.1 15.5 - - + +
18A ALA* 3.6 17.3 - - + -
19A PRO* 3.3 21.0 - - - +
29A ALA* 4.1 3.6 - - - +
31A VAL* 3.2 36.6 - - + -
64A PRO* 3.8 21.3 - - + -
75A LEU* 4.1 10.5 - - + -
78A VAL* 3.4 34.3 - - + -
79A THR* 1.3 76.0 - - - +
81A ALA* 1.3 64.0 + - - +
294A MET* 3.7 28.0 - - + -
297A LEU* 3.7 19.3 - - + -
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Residues in contact with ALA 81 (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 5.3 0.3 - - - +
18A ALA* 3.7 6.3 - - - +
19A PRO* 3.7 10.3 - - + +
21A VAL* 4.0 16.8 - - + -
27A TRP* 4.0 19.5 - - + -
29A ALA* 3.9 17.5 - - + -
31A VAL 2.9 5.9 + - - +
32A ALA* 3.3 3.0 - - + -
33A ALA* 2.9 25.3 + - - +
80A PHE* 1.3 78.8 - - - +
82A ASP* 1.3 61.0 + - - +
83A ALA 4.0 0.7 - - - -
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Residues in contact with ASP 82 (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 THR* 3.4 18.4 - - - -
15A PHE* 2.8 27.1 + - + +
18A ALA* 4.1 2.9 - - + +
19A PRO 3.0 13.4 + - - +
20A LEU* 3.1 11.2 - - + +
21A VAL* 2.9 25.2 + - - -
33A ALA* 3.8 6.6 - - - +
56A ARG* 2.7 36.5 + - - -
81A ALA* 1.3 75.3 - - - +
83A ALA* 1.3 56.7 + - - +
84A GLY* 2.8 27.8 + - - -
12E ILE* 3.8 7.4 - - - +
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Residues in contact with ALA 83 (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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21A VAL* 3.3 31.2 - - + +
22A GLN* 5.6 0.3 + - - -
23A PRO* 3.5 27.4 - - + +
27A TRP* 4.5 5.8 - - + -
32A ALA* 5.4 0.6 - - + +
33A ALA 2.8 18.6 + - - +
34A LEU* 4.0 4.4 - - + +
81A ALA 4.0 0.8 - - - -
82A ASP* 1.3 71.6 - - - +
84A GLY* 1.3 62.2 + - - +
85A ASP 3.9 1.4 + - - +
107A VAL* 3.7 29.6 - - + -
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Residues in contact with GLY 84 (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 LEU* 4.0 12.1 - - - +
34A LEU* 3.4 5.4 - - - +
35A GLY 2.9 21.7 + - - -
56A ARG* 3.0 12.8 + - - -
82A ASP* 2.8 18.0 + - - -
83A ALA* 1.3 80.8 - - - +
85A ASP* 1.3 59.0 + - - -
12E ILE* 4.3 8.5 - - - -
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Residues in contact with ASP 85 (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* 5.5 3.5 - - - +
34A LEU* 4.3 4.2 - - - +
35A GLY* 3.2 15.1 - - - +
37A PRO* 3.9 19.2 - - + +
52A PRO* 4.6 3.4 - - - +
53A ARG 5.7 0.2 + - - -
56A ARG* 2.8 37.9 + - - -
83A ALA 3.9 2.4 + - - +
84A GLY* 1.3 73.3 - - - -
86A VAL* 1.3 69.1 + - - +
87A ILE* 3.4 2.8 + - - +
6E HIS* 3.2 20.8 + - + -
9E TYR 4.3 2.6 - - - +
10E GLY* 3.7 6.2 - - - -
11E GLY* 2.8 36.2 + - - +
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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