Contacts of the helix formed by residues 1077 - 1081 (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 GLY1077 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060B HIS* 3.6 13.2 - - - -
1075B MET* 3.5 3.8 + - - +
1076B GLU* 1.3 81.1 - - - +
1078B ARG* 1.3 64.4 + - - -
1079B SER* 3.3 6.7 + - - -
1080B ARG* 3.1 7.0 + - - +
1081B ASP 3.0 3.3 + - - -
1082B GLY* 2.5 28.9 + - - -
1083B GLY 4.4 1.1 - - - -
1084B LEU* 5.9 0.9 - - - -
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Residues in contact with ARG1078 (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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897B ARG* 5.9 0.5 - - - +
898B THR 3.4 26.2 + - - +
899B SER* 3.7 18.9 - - - +
900B GLU* 5.0 2.4 - - - +
1056B ASP* 2.7 29.1 + - - -
1057B ASP* 2.6 40.7 + - - +
1058B LYS 5.5 0.2 - - - -
1059B ILE* 3.6 23.2 + - - +
1060B HIS* 3.2 36.5 + - + +
1077B GLY* 1.3 70.1 - - - -
1079B SER* 1.3 58.4 + - - +
1081B ASP* 2.7 29.5 + - - +
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Residues in contact with SER1079 (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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897B ARG* 4.8 18.4 - - - +
898B THR* 5.5 1.2 + - - -
1076B GLU* 5.4 2.8 - - - +
1077B GLY* 3.3 8.3 + - - -
1078B ARG* 1.3 75.4 - - - +
1080B ARG* 1.3 73.3 + - - +
54M THR 4.9 7.3 + - - -
56Y G 4.9 12.3 - - - -
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Residues in contact with ARG1080 (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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897B ARG* 5.5 8.3 - - - +
1066B PRO* 3.9 14.7 - - - +
1075B MET* 3.5 37.6 - - + +
1076B GLU 5.9 0.2 - - - +
1077B GLY 3.1 4.0 + - - +
1079B SER* 1.3 90.9 + - - +
1081B ASP* 1.3 72.3 - - - +
1082B GLY* 3.3 2.2 + - - -
27M TYR* 3.6 22.3 + - - +
50M SER* 3.5 29.7 + - - +
53M ARG* 3.6 39.3 + - - +
54M THR* 4.4 7.3 + - - +
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Residues in contact with ASP1081 (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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897B ARG* 4.8 15.0 - - - +
1060B HIS* 4.1 5.3 - - - -
1061B SER 4.7 1.6 - - - +
1062B ARG* 3.7 17.8 + - - +
1065B GLY* 5.5 0.2 - - - -
1066B PRO* 4.2 9.8 - - + +
1077B GLY 3.6 0.2 - - - -
1078B ARG* 2.7 27.4 + - - +
1080B ARG* 1.3 79.7 - - - +
1082B GLY* 1.3 62.2 + - - +
27M TYR* 3.7 23.1 - - + +
28M ARG* 4.0 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