Contacts of the helix formed by residues 830 - 837 (chain B) in PDB entry 2O8C
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 SER 830 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698B GLN 4.2 4.2 + - - -
699B GLU* 4.4 4.1 - - - -
702B SER* 3.9 14.4 + - - -
826B HIS* 3.0 21.2 + - - -
827B ASN* 3.5 19.1 - - - -
828B VAL 3.2 3.8 - - - +
829B GLY* 1.3 75.5 - - - +
831B PRO* 1.3 70.7 - - - +
832B LEU* 3.9 5.5 + - - +
833B LYS* 3.8 21.0 + - - +
834B SER* 3.4 20.6 + - - -
1034B ARG* 4.3 1.0 - - - -
1038B TYR* 5.0 0.9 - - - -
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Residues in contact with PRO 831 (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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645B GLU* 4.3 22.4 - - + +
702B SER* 6.5 0.2 - - - -
826B HIS* 6.4 0.2 - - + -
829B GLY 3.1 6.7 - - - +
830B SER* 1.3 84.0 - - - +
832B LEU* 1.3 69.3 - - + +
833B LYS 3.1 0.2 - - - -
834B SER* 2.8 25.2 + - - +
835B GLN* 3.1 20.0 + - + +
1034B ARG* 4.2 18.4 - - - +
1038B TYR* 3.6 36.3 - - + -
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Residues in contact with LEU 832 (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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640B GLU 3.8 15.7 - - - +
641B GLU* 3.9 24.2 - - + +
642B TYR* 4.0 19.3 - - + -
645B GLU* 5.3 8.6 + - + +
698B GLN* 3.7 47.5 - - + +
702B SER* 4.3 7.6 - - - -
830B SER* 3.5 7.8 - - - +
831B PRO* 1.3 83.1 - - + +
833B LYS* 1.3 62.5 + - - +
835B GLN* 3.3 25.5 + - - +
836B ASN* 3.6 14.5 - - - +
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Residues in contact with LYS 833 (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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515B ARG* 6.4 0.4 - - - +
695B LEU 5.0 0.2 + - - -
698B GLN* 3.4 16.8 - - + +
699B GLU* 2.8 41.7 + - + -
827B ASN* 4.4 11.5 + - - +
830B SER* 3.7 18.3 + - - +
831B PRO 3.1 0.6 - - - -
832B LEU* 1.3 76.8 - - - +
834B SER* 1.3 59.2 + - - +
835B GLN 2.9 11.3 + - - -
837B HIS* 3.0 68.7 + - + +
839B ASP* 4.6 13.0 + - - -
840B SER* 6.3 0.4 - - - -
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Residues in contact with SER 834 (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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830B SER 3.4 9.0 + - - -
831B PRO* 2.8 19.1 + - - +
833B LYS* 1.3 77.2 - - - +
835B GLN* 1.3 62.7 + - - +
840B SER* 3.7 22.4 + - - -
1034B ARG* 3.4 36.4 + - - -
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Residues in contact with GLN 835 (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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831B PRO* 3.1 19.3 + - + +
832B LEU* 3.3 35.0 - - - +
833B LYS 2.9 3.4 + - - -
834B SER* 1.3 80.7 - - - +
836B ASN* 1.3 65.4 + - + +
837B HIS 3.9 0.2 - - - -
840B SER* 4.8 1.7 + - - -
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Residues in contact with ASN 836 (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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698B GLN* 3.9 15.5 + - - +
832B LEU* 3.6 14.9 - - - +
835B GLN* 1.3 83.7 - - - +
837B HIS* 1.3 63.1 + - - +
838B PRO* 3.8 1.6 - - - +
840B SER* 4.7 0.7 - - - -
841B ARG* 2.8 28.4 + - - +
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Residues in contact with HIS 837 (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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514B CYS 3.4 24.7 - - - -
515B ARG* 6.3 0.2 - - - -
695B LEU* 2.9 35.1 + - + +
697B ASP* 6.1 0.7 - - - -
698B GLN* 3.8 16.6 - - + +
699B GLU* 6.3 0.2 - - + -
833B LYS* 3.0 52.7 + - + +
836B ASN* 1.3 80.1 + - - +
838B PRO* 1.4 72.6 - - + +
839B ASP* 3.1 32.9 + - + +
840B SER* 2.5 30.6 + - - +
841B ARG* 3.7 6.3 + - - -
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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