Contacts of the strand formed by residues 37 - 42 (chain I) in PDB entry 5XVO
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 37 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I MET* 4.2 3.5 - - - +
2I GLY* 3.9 12.2 + - - -
4I ARG* 3.8 6.5 - - + +
6I VAL* 4.2 16.8 - - + -
21I LEU* 4.1 25.6 - - + -
32I ILE* 3.7 24.0 - - + -
33I HIS 3.7 13.5 - - - +
34I LEU* 3.0 18.1 + - + +
35I SER 3.3 0.5 - - - +
36I GLU* 1.3 77.3 - - - +
38I ASP* 1.3 62.3 + - - +
39I VAL 3.7 24.2 - - - +
40I LEU* 4.4 4.9 - - + +
57I LEU* 5.2 4.0 - - + -
62I ILE* 3.6 37.5 - - + +
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Residues in contact with ASP 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I MET* 3.3 17.0 - - - +
2I GLY 3.6 22.5 - - - +
3I TRP* 4.0 4.5 - - - +
4I ARG 2.8 20.8 + - - +
5I THR* 5.1 2.8 + - - +
37I ILE* 1.3 74.8 - - - +
39I VAL* 1.3 66.0 + - + +
62I ILE* 3.7 4.0 - - - +
63I LEU 3.3 13.2 + - - -
84I HIS* 2.7 50.2 + - - -
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Residues in contact with VAL 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I ARG 3.1 3.4 + - - +
5I THR* 4.1 20.9 - - + +
6I VAL 2.8 28.2 + - - -
37I ILE* 3.7 7.2 - - - +
38I ASP* 1.3 101.9 - - + +
40I LEU* 1.3 70.8 + - - +
41I LEU* 4.4 2.0 - - + +
62I ILE* 4.2 0.2 - - - -
63I LEU* 3.4 26.0 - - + +
65I LEU* 4.5 4.7 - - + -
84I HIS* 4.0 14.4 - - + -
193I GLN* 4.2 28.3 - - + +
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Residues in contact with LEU 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I VAL* 3.6 33.2 - - + +
8I VAL* 4.0 14.8 - - + -
14I LEU* 4.5 9.4 - - + -
21I LEU* 4.6 15.7 - - + -
37I ILE* 4.9 4.5 - - + -
39I VAL* 1.3 74.5 - - - +
41I LEU* 1.3 61.4 + - - +
42I LEU* 3.9 21.0 + - + -
49I LEU* 6.1 1.1 - - + -
53I LEU* 5.3 0.7 - - + -
57I LEU* 3.6 31.6 - - + -
62I ILE* 3.9 11.8 - - + +
63I LEU 2.7 13.3 + - - +
64I VAL* 3.4 9.5 - - + +
65I LEU* 2.9 26.7 + - - +
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Residues in contact with LEU 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I THR* 5.1 0.9 - - + -
6I VAL 2.8 14.8 + - - +
7I VAL* 4.3 14.8 - - + -
8I VAL* 2.9 28.1 + - - +
39I VAL* 4.0 10.7 - - + -
40I LEU* 1.3 73.0 - - - +
42I LEU* 1.3 63.1 + - - +
43I GLU* 3.6 21.0 + - + +
65I LEU* 3.6 29.2 - - + -
67I CYS* 4.1 20.9 - - - -
73I PRO* 6.1 0.7 - - + -
189I ARG* 3.9 21.8 - - + +
193I GLN* 3.4 26.7 - - + +
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Residues in contact with LEU 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I VAL* 3.9 16.6 - - + -
14I LEU* 3.7 28.3 - - + -
40I LEU* 3.9 21.5 - - + +
41I LEU* 1.3 70.9 - - - +
43I GLU* 1.3 63.0 + - - +
44I THR 3.4 5.4 + - - +
47I ILE* 4.1 13.2 - - + -
49I LEU* 3.6 27.1 - - + -
64I VAL* 4.3 9.6 - - + -
65I LEU 3.0 14.7 + - - +
66I PHE* 3.8 26.9 - - + -
67I CYS* 3.2 25.2 + - - +
51J THR* 4.3 9.4 - - + -
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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