Contacts of the helix formed by residues 1031 - 1035 (chain B) in PDB entry 5JHN
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 VAL1031 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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996B TYR* 3.7 35.9 - - + -
1000B GLY* 3.6 41.5 - - - +
1016B GLU* 3.2 4.2 + - - -
1028B LYS 4.5 6.1 - - - +
1029B ASN 3.9 0.2 - - - -
1030B ARG* 1.3 77.4 - - - +
1032B VAL* 1.3 65.7 + - - +
1034B SER* 3.1 18.6 + - - -
1035B GLY 3.8 6.6 + - - +
1037B LYS* 5.6 0.2 + - - -
1063B PHE* 3.8 26.6 - - + -
1139B PHE* 4.5 1.3 - - + -
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Residues in contact with VAL1032 (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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996B TYR* 3.7 11.0 - - - +
1016B GLU* 2.8 22.7 + - - +
1031B VAL* 1.3 73.0 - - - +
1033B GLN* 1.3 61.2 + - - +
1034B SER 3.0 0.2 - - - -
1035B GLY* 3.1 15.9 + - - -
1063B PHE* 4.0 27.0 - - + -
1066B GLU* 4.6 14.3 - - - +
1124B VAL* 4.2 6.7 - - + -
1126B MET* 3.7 25.7 - - + +
1135B ARG* 5.1 3.3 + - + +
1137B ALA* 3.8 27.8 - - + -
1139B PHE* 3.8 13.7 - - + -
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Residues in contact with GLN1033 (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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930A TYR* 5.7 0.3 - - - -
1016B GLU* 2.9 29.6 + - - +
1017B CYS 3.0 22.3 + - - +
1025B ARG* 3.4 25.0 + - - +
1030B ARG* 3.0 52.5 + - + +
1032B VAL* 1.3 75.8 - - - +
1034B SER* 1.3 58.7 + - - +
1035B GLY* 3.3 0.8 + - - -
1126B MET* 3.4 25.9 - - + +
1127B LEU* 5.0 12.5 - - + +
1135B ARG* 5.2 5.2 - - - +
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Residues in contact with SER1034 (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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932B ASN* 2.9 19.9 + - - +
1025B ARG* 3.2 25.7 + - - +
1030B ARG* 2.9 14.8 + - - +
1031B VAL* 3.1 12.1 + - - -
1032B VAL 3.0 1.2 - - - -
1033B GLN* 1.3 77.8 - - - +
1035B GLY* 1.3 58.6 + - - +
1037B LYS* 3.9 21.4 + - - -
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Residues in contact with GLY1035 (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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931B GLU* 5.7 1.3 - - - -
932B ASN* 3.4 3.4 - - - -
1031B VAL 3.8 3.1 + - - +
1032B VAL 3.1 14.6 + - - -
1033B GLN 3.3 1.6 - - - -
1034B SER* 1.3 80.1 - - - +
1036B ILE* 1.3 66.1 + - - -
1037B LYS* 3.5 10.7 + - - +
1063B PHE* 3.5 21.8 - - - -
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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