Contacts of the strand formed by residues 35 - 39 (chain B) in PDB entry 1XV2
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 GLY 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B LEU* 1.3 79.8 - - - +
36B ILE* 1.3 69.6 + - - +
47B ILE* 3.8 0.9 - - - -
48B PHE* 2.9 37.7 + - - +
75B SER 3.2 12.8 - - - -
156B VAL* 3.8 7.8 - - - +
157B GLY 5.8 0.2 - - - -
158B PHE* 3.7 11.2 - - - -
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Residues in contact with ILE 36 (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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35B GLY* 1.3 81.2 - - - +
37B ALA* 1.3 65.8 + - - +
46B VAL 3.5 5.2 - - - -
48B PHE* 3.7 4.0 - - - -
73B TYR* 5.8 2.0 - - + -
75B SER* 2.9 46.7 + - - +
156B VAL 3.7 15.0 - - - +
157B GLY* 4.5 2.5 - - - -
158B PHE* 4.1 11.7 - - + -
173B HIS* 3.2 57.4 - - + +
175B HIS* 3.4 37.7 - - + +
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Residues in contact with ALA 37 (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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36B ILE* 1.3 81.4 - - - +
38B THR* 1.3 68.3 + - - +
45B GLU* 3.9 1.4 - - - +
46B VAL* 2.9 38.1 + - + +
48B PHE* 3.8 10.8 - - + -
71B VAL* 4.5 3.8 - - + -
73B TYR* 3.3 22.9 - - - +
74B ALA* 3.6 13.2 - - + +
175B HIS* 3.6 11.3 - - - -
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.4 14.1 - - + -
37B ALA* 1.3 77.8 - - - +
39B LEU* 1.3 63.6 + - - +
42B SER* 3.2 32.3 + - - +
43B ASP 3.3 0.2 + - - -
44B GLY 2.9 22.8 + - - -
45B GLU* 5.8 0.4 - - - -
46B VAL* 3.7 11.9 - - - -
71B VAL* 3.0 24.9 - - - +
72B PRO* 3.1 28.7 - - + +
73B TYR* 3.5 7.3 + - + +
126B MSE 6.1 0.2 - - - -
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Residues in contact with LEU 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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25B ILE* 4.2 5.2 - - + -
38B THR* 1.3 77.6 + - - +
40B THR* 1.3 71.5 + - - +
42B SER* 2.7 18.2 + - - -
43B ASP* 3.2 19.8 + - + +
46B VAL* 4.0 9.9 - - + -
55B HIS* 3.5 35.9 - - + +
65B LEU* 4.1 13.2 - - + -
69B GLU* 3.7 26.7 - - + -
70B LYS 3.3 14.8 - - - +
71B VAL* 3.8 14.4 - - + -
72B PRO* 3.3 10.1 - - - +
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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