Contacts of the strand formed by residues 37 - 42 (chain A) in PDB entry 2VWK
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 TYR 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A PHE* 5.2 3.6 - + - -
35A GLU 3.6 15.9 - - - -
36A PRO* 1.3 75.6 - - + +
38A ILE* 1.3 74.2 + - - +
39A TYR* 3.5 35.4 + + - -
84A LYS* 3.8 34.1 - - + -
85A LEU 3.1 17.9 - - - +
86A TYR* 4.2 12.1 - + + -
87A PHE* 4.0 2.5 - - - -
93A GLN* 3.8 6.5 + - - +
111A GLU* 3.7 10.5 + - + +
119A ARG* 3.3 37.5 + - - +
123A ASP* 2.5 32.3 + - - -
362A TYR* 3.8 9.8 - + - -
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Residues in contact with ILE 38 (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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37A TYR* 1.3 81.0 - - - +
39A TYR* 1.3 75.9 + - - +
84A LYS* 3.4 7.3 - - - +
85A LEU* 2.8 55.3 + - + -
87A PHE* 4.0 18.2 - - + -
93A GLN* 3.6 29.6 - - + +
96A ILE* 5.9 0.4 - - + -
97A ARG* 5.3 6.3 - - + -
100A ILE* 4.7 7.0 - - + -
109A ILE* 4.3 26.0 - - + -
110A TYR 3.5 11.7 - - - +
111A GLU 4.1 1.3 - - - -
112A TYR* 3.7 15.9 - - + -
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Residues in contact with TYR 39 (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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37A TYR* 3.5 28.6 + + - -
38A ILE* 1.3 78.8 - - - +
40A ALA* 1.3 61.5 + - - +
71A VAL* 3.9 9.9 - - + -
73A LYS* 3.3 32.9 + - + -
82A VAL* 3.8 24.2 - - + -
83A TRP 3.2 4.7 - - - +
84A LYS* 3.6 34.6 - - + -
85A LEU* 5.0 0.2 - - - -
109A ILE* 3.3 7.4 - - - +
110A TYR* 2.9 34.5 + - + +
111A GLU* 3.5 37.6 + - + -
362A TYR* 5.3 6.1 - - - -
367A LEU* 3.7 25.6 - - + -
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Residues in contact with ALA 40 (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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39A TYR* 1.3 77.0 - - - +
41A LEU* 1.3 61.0 + - - +
42A LEU* 3.8 18.9 + - + -
51A VAL* 5.8 0.7 - - + -
82A VAL* 3.6 6.8 - - - +
83A TRP* 2.8 35.0 + - + +
85A LEU* 3.9 26.2 - - + -
100A ILE* 4.9 2.2 - - + -
106A VAL* 4.9 3.8 - - + -
108A ASP 3.6 8.3 - - - +
109A ILE* 4.3 10.3 - - + +
110A TYR* 5.1 0.2 - - - -
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Residues in contact with LEU 41 (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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40A ALA* 1.3 71.7 - - - +
42A LEU* 1.3 64.4 + - - +
80A ILE* 4.0 28.3 - - + -
81A GLU 3.5 22.7 - - - +
82A VAL* 4.3 4.0 - - + +
106A VAL* 3.5 4.7 - - - +
107A VAL* 2.7 60.5 + - + -
108A ASP* 2.9 22.6 + - - +
110A TYR* 4.2 16.5 - - + +
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Residues in contact with LEU 42 (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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40A ALA* 3.8 15.6 + - + +
41A LEU* 1.3 91.2 - - - +
43A LYS* 1.3 64.9 + - - +
44A ASP 4.0 17.2 - - - +
45A ASP* 4.5 1.1 - - - +
47A ALA* 4.2 5.2 - - + -
48A ILE* 3.8 34.8 - - + +
51A VAL* 4.3 8.5 - - + -
81A GLU 5.2 1.6 + - - +
83A TRP* 3.4 39.3 - - + +
105A ALA 3.1 8.5 - - - +
106A VAL* 3.6 28.7 - - + -
107A VAL* 4.5 3.2 - - - +
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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