Contacts of the strand formed by residues 38 - 41 (chain B) in PDB entry 2VKM
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 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B MET* 4.0 21.1 - - + -
20B VAL* 4.1 16.4 - - + -
29B ILE* 3.9 24.0 - - + -
36B SER 4.2 1.6 + - - -
37B ASN* 1.3 72.8 + - - +
39B ALA* 1.3 60.6 + - - +
40B VAL* 4.1 15.7 - - + -
85B VAL* 3.9 27.6 - - + -
98B ASN 3.4 25.0 - - - +
99B ILE* 3.7 16.2 - - + -
100B ALA* 3.0 24.6 + - - +
118B ILE 3.3 13.7 - - - -
119B LEU* 4.0 11.9 - - + -
120B GLY 4.5 2.2 - - - +
133B LEU* 6.2 0.2 - - - +
135B PRO* 6.1 0.2 - - - +
136B PHE* 4.4 29.7 - + + +
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Residues in contact with ALA 39 (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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37B ASN 3.7 0.8 + - - +
38B PHE* 1.3 76.0 - - - +
40B VAL* 1.3 65.4 + - - +
76B TRP* 3.3 36.8 - - + -
99B ILE* 5.1 0.2 - - - -
100B ALA* 3.3 12.3 - - + +
102B ILE* 3.7 14.6 - - + -
117B GLY* 3.1 1.6 - - - -
118B ILE* 2.7 46.7 + - + +
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 5.1 3.4 - - + -
27B LEU* 4.1 14.4 - - + -
29B ILE* 3.8 25.1 - - + -
38B PHE* 4.1 16.2 - - + -
39B ALA* 1.3 80.8 - - - +
41B GLY* 1.3 67.8 + - - +
42B ALA 3.2 0.2 + - - -
52B TYR* 3.4 41.5 - - + -
99B ILE* 4.2 12.3 - - + -
100B ALA 3.1 6.0 + - - +
101B ALA* 3.8 0.6 - - - -
102B ILE* 2.9 26.2 + - - -
116B GLU 3.6 8.7 - - - +
117B GLY* 3.8 0.2 - - - -
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Residues in contact with GLY 41 (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 LEU* 5.2 0.2 - - - +
40B VAL* 1.3 74.1 - - - +
42B ALA* 1.3 57.7 + - - -
43B ALA 5.0 0.2 - - - -
48B LEU* 3.8 22.9 - - - -
51B TYR* 3.3 10.0 - - - +
52B TYR* 2.9 25.3 + - - +
102B ILE* 4.1 4.9 - - - -
109B PHE* 3.8 11.9 - - - -
116B GLU 2.8 19.1 + - - -
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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