Contacts of the strand formed by residues 1016 - 1019 (chain B) in PDB entry 4E4N
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 GLN1016 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935B GLU* 3.1 50.7 + - + +
936B ASN* 4.0 2.9 - - - +
983B TYR* 3.9 1.9 - - - -
986B GLN* 3.2 10.1 - - - +
1011B VAL 3.8 0.3 - - - -
1012B GLU* 2.8 55.5 + - + +
1013B SER* 3.1 19.6 + - - +
1014B GLU 3.6 0.4 - - - -
1015B HIS* 1.3 80.8 - - + +
1017B VAL* 1.3 68.8 + - - +
1018B LYS* 4.2 4.2 - - - +
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Residues in contact with VAL1017 (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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936B ASN* 3.0 25.0 - - - +
964B LEU* 4.0 21.1 - - + -
983B TYR* 3.7 52.0 - - + +
986B GLN* 2.8 21.3 + - + +
987B ILE* 3.9 16.8 - - + +
1009B VAL* 3.7 7.4 - - + -
1010B LEU 3.1 14.8 - - - +
1011B VAL* 4.2 5.2 - - + -
1012B GLU 4.3 0.2 - - - +
1016B GLN* 1.3 76.5 - - - +
1018B LYS* 1.3 68.2 + - - +
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Residues in contact with LYS1018 (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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934B HIS 5.6 0.2 + - - -
935B GLU* 3.5 24.0 + - - +
936B ASN* 3.3 10.5 - - - -
937B ILE 3.8 11.0 + - - +
938B VAL* 3.8 12.1 - - + +
939B LYS* 3.1 26.3 - - - +
957B GLU* 2.8 30.3 + - - +
959B LEU* 4.2 15.9 - - + -
987B ILE* 6.3 0.4 - - - -
1009B VAL* 3.5 5.8 - - - -
1010B LEU* 2.7 43.1 + - + +
1012B GLU* 3.7 29.7 + - + -
1016B GLN* 4.2 5.6 - - - +
1017B VAL* 1.3 80.9 - - - +
1019B ILE* 1.3 62.3 + - - +
1020B GLY 3.3 0.3 + - - -
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Residues in contact with ILE1019 (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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936B ASN 2.8 17.0 + - - +
937B ILE* 3.7 4.2 - - + -
938B VAL* 3.0 25.8 + - - +
987B ILE* 4.0 17.5 - - + +
990B GLY* 3.7 12.1 - - - +
991B MET* 3.4 50.0 - - + +
994B LEU* 5.7 0.9 - - + -
1001B HIS* 3.6 29.8 - - + +
1004B LEU* 5.0 8.5 - - + -
1008B ASN* 3.8 7.9 - - + +
1009B VAL* 4.6 4.5 - - + +
1018B LYS* 1.3 71.3 - - - +
1020B GLY* 1.3 61.2 + - - +
1021B ASP 3.7 1.3 - - - +
1022B PHE* 3.7 23.0 - - + -
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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