Contacts of the strand formed by residues 20 - 24 (chain J) 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 HIS 20 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16J TYR* 3.5 11.9 - - - -
17J LYS 2.8 32.5 + - - +
18J ASN* 3.1 9.8 + - - +
19J ASN* 1.3 78.2 - - - +
21J LEU* 1.3 69.4 + - - +
31J LEU* 4.2 29.9 - - + +
32J ILE 3.3 6.7 - - - +
33J HIS* 3.1 53.9 - + + +
34J LEU* 4.4 1.1 - - - -
33M ILE* 3.4 34.0 + - + +
36M GLY* 3.9 7.2 + - - -
37M PHE 5.0 4.7 - - - -
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Residues in contact with LEU 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J VAL* 4.4 20.4 - - + -
14J LEU* 4.6 13.5 - - + -
15J SER 3.8 2.2 - - - +
20J HIS* 1.3 72.2 - - - +
22J VAL* 1.3 67.1 + - - +
23J PHE* 5.0 1.1 - - + -
30J GLU 3.7 1.0 - - - +
31J LEU* 3.4 4.9 - - - -
32J ILE* 2.7 46.5 + - + +
34J LEU* 4.2 10.7 - - + +
37J ILE* 4.1 23.8 - - + -
40J LEU* 4.6 19.7 - - + -
53J LEU* 3.4 39.0 - - + -
57J LEU* 5.2 0.9 - - + -
106M LEU* 4.9 9.4 - - + -
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Residues in contact with VAL 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J LYS 3.4 2.4 - - - +
14J LEU* 3.3 7.3 - - - +
15J SER* 2.8 54.0 + - - +
16J TYR 4.2 0.2 - - - -
17J LYS* 3.8 36.6 - - + +
20J HIS 4.0 2.2 - - - +
21J LEU* 1.3 78.9 - - - +
23J PHE* 1.3 61.0 + - - +
24J LYS* 4.0 28.9 - - + -
29J GLN* 5.9 1.8 - - + -
30J GLU 3.7 2.7 - - - +
31J LEU* 3.6 28.0 - - + -
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Residues in contact with PHE 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J VAL* 4.1 5.8 - - + -
10J LYS* 4.6 8.3 - - + -
12J SER* 3.3 25.8 - - - -
13J LYS 3.9 1.3 - - - -
14J LEU* 3.6 19.3 - - + -
21J LEU* 4.0 4.6 + - + -
22J VAL* 1.3 71.4 - - - +
24J LYS* 1.3 61.6 + - - +
25J ALA* 3.8 29.2 - - + -
28J HIS* 4.0 22.9 - + - -
29J GLN* 3.3 5.7 - - - +
30J GLU* 2.9 51.5 + - + +
32J ILE* 6.1 0.4 - - + -
106M LEU* 3.1 57.0 - - + -
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Residues in contact with LYS 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J SER* 3.3 5.0 - - - -
13J LYS* 2.8 53.0 + - + +
15J SER* 5.1 5.4 - - - +
22J VAL* 4.0 22.4 - - + -
23J PHE* 1.3 74.2 - - - +
25J ALA* 1.3 62.1 + - - +
29J GLN* 3.0 46.6 + - + +
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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