Contacts of the strand formed by residues 46 - 50 (chain B) in PDB entry 1XZQ
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 ILE 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 4.5 13.5 - - + -
36B THR* 3.7 23.3 - - - +
38B SER* 4.9 11.4 - - - +
39B LYS 3.9 6.5 - - - +
40B ILE* 3.3 44.6 - - + +
41B VAL 3.9 6.1 - - - +
44B LYS* 2.9 28.6 + - + +
45B ALA* 1.3 81.3 - - - +
47B HIS* 1.3 64.4 + - - +
61B VAL* 3.0 16.3 - - - +
62B VAL* 3.1 25.6 + - + +
64B PHE* 4.1 13.0 - - + -
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Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 6.6 0.2 - - - -
451A FON 3.2 77.7 - + + +
36B THR* 3.0 19.0 + - - -
37B ARG* 4.3 10.1 + - + +
38B SER* 5.2 3.3 + - - -
45B ALA 3.5 3.8 + - - +
46B ILE* 1.3 76.9 - - - +
48B GLY* 1.3 95.5 + - - +
49B TRP* 4.6 6.7 - + - -
59B GLU* 3.4 25.9 + - + -
60B VAL 3.5 8.7 + - - -
61B VAL* 4.4 7.0 - - + +
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Residues in contact with GLY 48 (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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34B LEU* 4.5 5.6 - - - +
35B ARG 3.7 9.0 - - - -
36B THR* 4.3 6.3 - - - -
37B ARG* 5.6 2.5 - - - -
46B ILE* 4.4 1.4 + - - +
47B HIS* 1.3 90.9 + - - +
49B TRP* 1.3 75.7 + - - -
59B GLU* 3.6 2.1 - - - -
60B VAL* 3.1 31.3 + - - +
61B VAL* 4.9 0.2 - - - +
62B VAL 5.4 0.4 - - - +
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Residues in contact with TRP 49 (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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142A LEU* 4.0 20.6 - - + -
145A LEU* 4.0 18.4 - - + -
146A LYS* 3.5 40.2 - - + -
33B HIS 3.5 0.2 - - - +
34B LEU* 3.3 6.4 - - - +
35B ARG* 2.6 79.3 + - - +
37B ARG* 5.9 4.3 - - - -
47B HIS* 4.6 4.6 - + - -
48B GLY* 1.3 89.9 + - - -
50B ILE* 1.3 62.9 + - - +
51B HIS 4.1 0.2 - - - -
56B ASP* 3.8 19.7 - - + +
58B ASP 3.6 18.2 - - - -
59B GLU* 3.7 41.7 + - + +
60B VAL* 4.7 0.4 - - - -
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Residues in contact with ILE 50 (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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30B VAL* 4.9 5.2 - - + +
33B HIS* 3.1 9.9 - - + +
34B LEU* 3.3 36.6 - - + -
49B TRP* 1.3 71.9 - - - +
51B HIS* 1.3 54.9 + - - +
56B ASP* 3.5 3.9 - - - +
57B VAL* 2.6 47.7 + - + +
58B ASP 2.9 10.0 + - - +
60B VAL* 3.5 29.2 - - + -
62B VAL* 4.4 6.1 - - + -
79B VAL* 5.1 4.7 - - + -
91B LEU* 3.6 25.6 - - + -
94B LEU* 3.8 17.0 - - + -
95B PHE* 4.9 12.8 - - + -
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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