Contacts of the strand formed by residues 34 - 39 (chain B) in PDB entry 1XAH
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 SER 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 3.0 35.6 - - - +
31B PHE* 3.6 13.9 - - - +
33B GLN* 1.3 79.3 + - - +
35B PHE* 1.3 58.1 + - - +
36B LEU 3.9 0.2 - - - -
58B ASN* 2.8 23.3 + - - +
59B VAL* 3.1 9.2 - - - +
60B HIS* 2.7 31.9 + - - -
93B ALA* 3.5 7.2 - - - -
95B ILE* 4.3 8.7 - - - -
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Residues in contact with PHE 35 (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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33B GLN* 4.0 17.0 - - + -
34B SER* 1.3 72.4 - - - +
36B LEU* 1.3 61.3 + - - +
37B LEU* 3.2 21.6 + - + +
60B HIS* 3.3 25.1 - + + +
62B VAL* 4.0 13.9 - - + -
83B ILE* 3.6 23.3 - - + -
86B HIS* 3.6 38.6 - + + -
88B VAL* 3.5 33.7 - - + -
92B THR* 3.7 22.4 - - + -
93B ALA 2.9 9.9 + - - -
94B ILE* 3.6 10.7 - - + -
95B ILE* 2.9 27.8 + - - +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 6.1 2.9 - - + -
34B SER 3.8 1.8 + - - -
35B PHE* 1.3 70.2 - - - +
37B LEU* 1.3 62.5 + - - +
38B ILE* 3.2 10.3 + - + -
50B PHE* 4.4 32.8 - - + -
59B VAL* 4.5 15.7 - - + +
60B HIS 2.5 16.7 + - - +
61B LYS* 3.4 34.1 - - + +
62B VAL 2.8 21.2 + - - -
95B ILE* 3.6 23.1 - - + -
97B VAL* 3.5 28.5 - - + -
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Residues in contact with LEU 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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35B PHE* 3.6 21.5 - - + +
36B LEU* 1.3 70.3 - - - +
38B ILE* 1.3 58.9 + - - +
62B VAL* 3.3 37.9 - - + +
64B ILE* 4.4 11.3 - - + +
79B THR* 4.1 18.8 - - + -
83B ILE* 4.0 9.9 - - + -
94B ILE* 4.1 9.4 - - + -
95B ILE 2.8 12.5 + - - +
96B ALA* 3.6 1.6 - - - -
97B VAL* 2.8 26.7 + - - +
102B THR* 5.2 1.4 + - - -
105B PHE* 4.4 10.1 - - + -
106B ALA* 3.6 36.9 - - + +
109B VAL* 4.6 4.3 - - + -
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Residues in contact with ILE 38 (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 LEU* 4.0 3.8 - - + +
37B LEU* 1.3 74.9 - - - +
39B ASP* 1.3 74.2 + - - +
42B VAL* 4.1 6.7 - - + +
43B ASN* 3.7 25.8 - - + +
46B PHE 5.3 0.4 - - - +
50B PHE* 3.7 21.8 - - + -
61B LYS* 3.5 20.6 - - + -
62B VAL 3.0 4.4 + - - -
63B ILE* 3.2 32.2 - - + +
64B ILE* 3.1 24.7 + - - +
97B VAL* 3.4 38.1 - - + +
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Residues in contact with ASP 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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38B ILE* 1.3 76.2 - - - +
40B GLU* 1.3 59.7 + - - +
41B TYR 3.1 10.0 + - - -
42B VAL* 3.1 20.7 + - + +
43B ASN* 2.8 33.3 + - - +
64B ILE* 4.1 5.1 - - - +
65B PRO 4.1 0.2 - - - -
66B ALA* 3.4 9.6 - - - +
67B GLY* 3.0 26.2 + - - -
97B VAL 3.3 5.5 + - - +
99B GLY 5.1 0.5 + - - -
102B THR* 3.3 28.7 - - + +
401B NAD 3.0 29.9 + - - -
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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