Contacts of the helix formed by residues 1054 - 1059 (chain B) in PDB entry 5IYB
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 MET1054 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733B MET* 3.4 21.1 - - + -
749B HIS* 3.3 41.1 - - + +
808B SER* 4.1 5.2 - - - +
809B VAL 5.9 0.2 - - - +
810B PHE* 5.0 0.7 - - + -
927B ARG* 3.5 48.7 - - + +
930B GLN* 5.6 1.8 - - - +
933B ASP* 3.4 11.9 - - + +
1050B ARG* 3.8 20.6 - - - +
1051B LEU 4.4 5.6 - - - +
1052B LYS 2.7 20.0 + - - +
1053B HIS* 1.3 75.7 - - - +
1055B VAL* 1.3 65.4 + - - +
1056B ASP* 3.4 3.1 - - + +
1057B ASP* 3.5 26.5 + - - +
1058B LYS* 3.8 7.8 + - - +
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Residues in contact with VAL1055 (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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365A THR* 4.2 1.8 - - - +
366A VAL* 4.0 17.7 - - + -
480A SER* 3.6 31.6 - - - +
481A THR* 3.6 19.1 - - + -
930B GLN* 3.5 17.7 - - + +
931B ILE 3.7 15.0 - - - +
932B GLY* 3.6 18.1 + - - -
933B ASP* 2.7 20.4 + - - +
1053B HIS 3.6 1.2 + - - -
1054B MET* 1.3 68.3 - - - +
1056B ASP* 1.3 71.2 + - + +
1057B ASP 3.1 2.2 - - - -
1058B LYS* 3.1 12.9 + - - +
1059B ILE* 3.2 11.4 + - - +
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Residues in contact with ASP1056 (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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480A SER* 5.6 6.0 + - - -
899B SER* 4.8 8.0 - - - -
900B GLU* 4.3 21.8 + - - +
927B ARG* 3.7 26.0 + - - +
930B GLN* 4.2 15.2 - - - +
1054B MET* 3.4 1.9 - - + +
1055B VAL* 1.3 82.9 - - + +
1057B ASP* 1.3 52.0 + - - +
1059B ILE* 3.4 18.2 - - - +
1078B ARG* 2.7 34.4 + - - -
1K MET* 5.8 5.9 - - - -
2K ASN 6.0 0.2 + - - -
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Residues in contact with ASP1057 (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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749B HIS* 5.0 4.3 + - - -
810B PHE* 4.9 8.9 - - - -
927B ARG* 2.5 30.5 + - - -
1052B LYS 4.1 15.6 - - - +
1053B HIS* 6.1 0.4 - - - -
1054B MET* 3.5 17.4 + - - +
1055B VAL 3.1 0.8 - - - -
1056B ASP* 1.3 75.7 - - - +
1058B LYS* 1.3 58.0 + - + +
1078B ARG* 2.6 31.1 + - - +
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Residues in contact with LYS1058 (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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364A ARG* 4.1 21.6 + - + +
365A THR* 4.8 4.3 - - - -
366A VAL* 4.0 29.4 - - + +
498A GLY 5.4 5.8 - - - +
500A GLU* 5.3 15.0 - - + -
1053B HIS* 4.4 25.7 + - - +
1054B MET 3.8 7.8 + - - +
1055B VAL 3.1 7.8 + - - +
1057B ASP* 1.3 78.8 - - + +
1059B ILE* 1.3 66.2 + - - +
1060B HIS* 3.7 6.6 + - - +
1078B ARG* 5.5 0.2 - - - -
54Y A 5.1 11.3 + - - -
55Y G 4.4 13.7 + - - -
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Residues in contact with ILE1059 (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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364A ARG 3.8 4.5 - - - -
365A THR* 3.9 11.9 + - - +
381A PRO* 4.5 0.9 - - + -
383A SER* 4.0 11.4 - - - +
384A ILE* 3.6 35.7 - - + -
480A SER* 3.6 35.9 - - - +
1055B VAL 3.2 10.6 + - - +
1056B ASP* 3.4 29.8 - - - +
1058B LYS* 1.3 78.7 - - - +
1060B HIS* 1.3 65.8 + - - +
1078B ARG* 3.6 22.6 + - - +
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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