Contacts of the strand formed by residues 59 - 64 (chain B) in PDB entry 1XAI
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 VAL 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 3.8 23.1 - - + -
34B SER* 3.2 22.0 - - - +
36B LEU* 4.5 15.3 - - + -
53B ILE* 3.2 24.7 - - + +
54B LEU* 3.6 44.8 - - + +
56B TYR* 3.7 15.9 + - + +
58B ASN* 1.3 78.4 - - + +
60B HIS* 1.3 73.2 + - - +
95B ILE* 6.4 0.7 - - + -
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 4.6 10.1 - - + -
34B SER 3.0 6.2 + - - -
35B PHE* 3.4 39.9 - + + -
36B LEU* 2.7 27.9 + - - +
54B LEU* 5.3 0.2 - - - -
56B TYR 5.5 0.4 - - - -
57B GLU 4.4 9.2 + - - -
58B ASN 3.4 15.6 + - - -
59B VAL* 1.3 91.5 - - - +
61B LYS* 1.3 63.2 + - - +
62B VAL* 3.7 2.2 + - + +
82B TYR* 6.2 1.6 - - + -
86B HIS* 3.6 24.4 - + + +
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.6 12.3 - - + -
38B ILE* 3.7 22.2 - - + -
43B ASN* 3.2 30.8 + - - +
47B ALA 5.6 3.4 + - - -
54B LEU* 3.8 34.4 - - + +
60B HIS* 1.3 73.2 - - - +
62B VAL* 1.3 64.5 + - - +
63B ILE* 3.6 26.8 + - + +
82B TYR* 5.0 6.8 + - - -
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Residues in contact with VAL 62 (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 PHE* 4.0 14.8 - - + -
36B LEU 2.5 14.7 + - - +
37B LEU* 3.2 15.9 - - + -
38B ILE* 2.8 26.7 + - - +
60B HIS* 4.2 4.3 - - + +
61B LYS* 1.3 76.7 - - - +
63B ILE* 1.3 65.7 + - - +
64B ILE* 3.7 10.6 + - + -
79B THR* 4.2 25.8 - - + +
82B TYR* 4.4 16.8 - - + -
83B ILE* 3.6 24.9 - - + -
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Residues in contact with ILE 63 (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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38B ILE* 3.4 18.2 - - + +
39B ASP 4.3 0.9 - - - +
40B GLU* 3.6 34.5 - - + -
43B ASN* 3.9 20.9 - - - +
61B LYS* 3.6 30.7 + - + +
62B VAL* 1.3 76.0 - - - +
64B ILE* 1.3 65.0 + - - +
75B GLN* 5.5 1.0 + - - -
78B GLU* 5.8 0.2 - - - +
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.4 15.3 - - + -
38B ILE 3.5 9.1 + - - +
39B ASP 4.8 0.9 - - - +
40B GLU* 3.2 22.7 + - - +
62B VAL* 4.3 17.5 - - + +
63B ILE* 1.3 77.4 - - - +
65B PRO* 1.3 82.3 - - + +
70B THR* 3.3 10.3 - - + +
75B GLN* 4.7 2.2 - - - +
79B THR* 4.0 10.3 - - - +
102B THR* 3.7 35.2 - - + +
105B PHE* 3.4 40.2 - - + -
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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
------------------------------------------------------------
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