Contacts of the strand formed by residues 38 - 42 (chain A) in PDB entry 2VF7
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 LEU 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ALA* 1.3 68.1 - - - +
39A VAL* 1.3 57.9 + - - +
40A VAL* 4.3 7.9 - - + -
421A LEU* 4.5 19.1 - - + +
424A LEU* 4.2 21.8 - - + -
428A LYS* 3.9 5.5 - - + +
434A LEU* 4.0 20.2 - - + -
436A VAL* 3.7 30.5 - - + -
443A VAL* 4.9 3.8 - - + -
446A ARG 4.2 7.9 - - - +
447A ALA* 3.7 26.8 - - + +
448A ASP* 3.0 39.4 + - - +
449A TRP 3.4 7.4 + - - +
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Residues in contact with VAL 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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33A VAL* 4.3 4.9 - - + -
34A PRO* 3.6 30.5 - - + +
37A ALA* 4.1 6.3 - - + +
38A LEU* 1.3 74.8 - - - +
40A VAL* 1.3 55.8 + - - +
41A PHE* 3.9 19.6 - - + -
434A LEU 2.9 16.3 + - - +
435A PHE* 3.5 13.4 - - + -
436A VAL* 2.8 34.0 + - - +
449A TRP* 3.5 37.0 - - + +
451A VAL* 4.0 12.8 - - + -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.3 6.5 - - + -
39A VAL* 1.3 76.9 - - - +
41A PHE* 1.3 64.3 + - - +
42A THR* 3.4 22.3 + - + -
436A VAL* 3.0 18.8 - - + +
438A GLU* 3.8 19.7 - - + -
443A VAL* 4.2 19.7 - - + -
444A ILE* 4.0 11.4 - - + -
447A ALA* 3.5 27.4 - - + -
449A TRP 3.1 7.0 + - - +
450A LEU* 3.3 9.2 - - + +
451A VAL 2.9 24.4 + - - -
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Residues in contact with PHE 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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31A VAL* 6.0 0.9 - - + -
33A VAL* 4.5 7.2 - - + -
39A VAL* 3.9 19.7 - - + -
40A VAL* 1.3 72.0 - - - +
42A THR* 1.3 62.1 + - - +
49A LYS* 3.4 23.5 - - + +
52A LEU* 4.2 25.1 - - + -
53A ALA* 4.1 17.0 - - + -
57A LEU* 3.9 26.5 - - + -
435A PHE* 3.5 33.2 - + + -
436A VAL 2.7 21.6 + - - +
437A VAL* 3.5 11.0 - - + -
438A GLU 3.4 22.2 + - - -
451A VAL* 3.4 31.2 - - + +
453A VAL* 5.4 1.8 - - + -
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Residues in contact with THR 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 VAL* 3.4 28.7 - - + +
41A PHE* 1.3 78.8 - - - +
43A GLY* 1.3 58.8 + - - +
49A LYS* 3.4 15.1 - - - +
438A GLU 3.8 7.9 - - - +
444A ILE* 3.8 24.7 - - + -
450A LEU* 3.5 17.2 - - + +
451A VAL 2.8 11.2 + - - +
452A ASP* 2.6 22.6 + - - +
453A VAL* 2.8 25.3 + - - +
481A THR* 3.4 13.9 + - - +
765A HIS* 5.8 1.1 - - - -
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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