Contacts of the helix formed by residues 833 - 838 (chain A) in PDB entry 2RFD
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 GLY 833 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738A GLU* 4.2 4.0 - - - +
742A MET* 4.2 12.2 - - - +
810A VAL 5.2 1.3 - - - -
811A HIS 4.3 9.3 + - - -
831A ASP 3.8 0.8 + - - -
832A PHE* 1.3 94.2 - - - +
834A LEU* 1.3 62.3 + - - +
835A ALA 3.4 2.0 - - - -
836A LYS* 3.8 17.0 + - - +
837A LEU* 3.2 21.3 + - - +
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Residues in contact with LEU 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A ALA* 6.4 2.0 - - + -
699A PHE 5.3 2.5 - - - +
721A LYS* 3.8 20.0 - - + +
723A LEU* 4.1 19.1 - - + -
742A MET* 4.4 8.1 - - + -
764A LEU* 3.5 32.3 - - + -
831A ASP* 3.6 41.5 + - + +
832A PHE 3.1 3.2 + - - +
833A GLY* 1.3 76.7 - - - +
835A ALA* 1.3 61.0 + - - +
837A LEU* 2.8 10.8 + - + +
838A LEU* 2.8 43.6 + - + +
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Residues in contact with ALA 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811A HIS 4.3 5.4 - - - +
812A ARG* 4.2 26.4 + - + -
813A ASP* 4.4 16.2 - - + -
831A ASP 4.7 2.5 + - - +
833A GLY* 3.4 0.8 - - - +
834A LEU* 1.3 78.8 - - - +
836A LYS* 1.3 62.3 + - - +
838A LEU* 3.0 15.9 + - - +
839A GLY 3.2 19.5 + - - -
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Residues in contact with LYS 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SO4 3.6 42.9 + - - +
738A GLU* 3.4 30.6 + - - +
810A VAL 6.0 1.8 - - - +
811A HIS 5.3 0.6 + - - +
812A ARG* 4.5 31.9 - - + +
833A GLY* 3.8 15.9 + - - +
834A LEU 3.3 0.4 - - - -
835A ALA* 1.3 79.3 - - - +
837A LEU* 1.3 59.2 + - - +
838A LEU 3.6 0.2 + - - -
839A GLY* 4.0 6.2 + - - -
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Residues in contact with LEU 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A LEU* 3.9 25.4 - - + -
730A LYS* 6.0 2.4 - - + +
735A ILE* 3.5 47.9 - - + +
738A GLU* 3.6 30.5 - - + +
739A ALA 6.2 0.2 - - - +
742A MET* 4.8 9.9 - - - -
762A VAL* 5.6 0.4 - - + -
764A LEU* 4.7 8.3 - - + -
833A GLY 3.2 14.9 + - - +
834A LEU* 2.8 19.9 + - + +
836A LYS* 1.3 78.9 - - - +
838A LEU* 1.3 67.4 + - + +
839A GLY 3.6 1.2 + - - -
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Residues in contact with LEU 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A ALA* 6.3 0.2 - - + -
699A PHE* 3.2 35.0 - - + +
723A LEU* 3.6 44.9 - - + -
724A ARG 4.7 9.6 - - - +
725A GLU 5.6 2.9 - - - +
729A PRO* 6.3 1.6 - - - -
762A VAL* 5.7 0.9 - - + -
834A LEU* 2.8 25.5 + - + +
835A ALA* 3.0 4.6 + - - +
837A LEU* 1.3 92.2 - - + +
839A GLY* 1.3 65.3 + - - +
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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