Contacts of the helix formed by residues 871 - 878 (chain A) in PDB entry 6C90
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 GLU 871 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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862A GLY* 3.3 31.7 - - - +
863A PHE 2.8 18.8 + - - +
864A ALA* 3.7 13.1 - - - +
865A THR* 4.0 20.0 - - + +
870A ILE* 1.3 78.1 - - - +
872A MET* 1.3 61.5 + - - +
873A LYS* 3.9 4.9 - - + +
874A GLY* 2.8 15.8 + - - -
875A ARG* 3.1 12.4 + - - +
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Residues in contact with MET 872 (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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871A GLU* 1.3 75.5 + - - +
873A LYS* 1.3 62.0 + - - +
875A ARG* 3.1 32.2 + - + +
876A VAL* 3.1 25.9 + - + +
893A PHE* 4.8 2.9 - - + -
1013A ALA 3.7 22.9 - - - +
1014A ILE* 3.9 19.5 - - + -
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Residues in contact with LYS 873 (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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861A LEU* 2.7 28.5 + - - +
862A GLY* 3.6 18.8 - - - +
863A PHE* 3.9 24.0 - - + -
871A GLU* 3.9 1.5 - - + +
872A MET* 1.3 78.9 - - - +
874A GLY* 1.3 60.1 + - - +
876A VAL* 3.2 12.7 + - - +
877A ALA 3.3 8.7 + - - -
889A THR* 4.6 2.0 - - - +
890A GLU* 2.7 39.3 + - - +
893A PHE* 3.7 58.2 - - + +
894A ASN* 5.9 0.2 - - - +
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Residues in contact with GLY 874 (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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571A LEU* 3.9 5.0 - - - +
863A PHE* 3.6 31.8 + - - +
870A ILE* 3.6 11.4 - - - -
871A GLU 2.8 10.4 + - - -
873A LYS* 1.3 77.4 - - - +
875A ARG* 1.3 57.8 + - - +
877A ALA* 3.0 6.2 + - - +
878A CYS* 2.9 28.1 + - - -
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Residues in contact with ARG 875 (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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575A ARG* 3.7 19.0 + - - +
870A ILE* 3.7 38.5 + - + +
871A GLU 3.1 11.5 + - - +
872A MET* 3.1 37.2 + - + +
874A GLY* 1.3 76.7 - - - +
876A VAL* 1.3 62.6 + - - +
878A CYS* 3.4 19.7 + - + +
879A GLU* 3.5 14.6 - - - +
1013A ALA* 4.5 7.8 - - + +
1107A MLI 5.8 2.6 + - - -
668B THR 4.5 0.2 + - - -
669B GLY* 2.9 46.3 + - - +
670B ILE* 5.5 0.5 - - - +
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Residues in contact with VAL 876 (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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872A MET 3.1 14.7 + - - +
873A LYS 3.4 7.9 - - - +
874A GLY 3.1 0.6 - - - -
875A ARG* 1.3 76.5 - - - +
877A ALA* 1.3 64.2 + - - +
879A GLU* 3.1 23.4 + - - +
880A ILE* 4.0 3.1 + - - +
889A THR* 3.9 14.8 - - + -
892A MET* 3.9 16.8 - - + -
893A PHE* 4.0 16.8 - - + -
1010A ALA* 3.7 36.1 - - + +
1013A ALA* 4.5 2.9 - - + -
1014A ILE* 3.7 26.7 - - + -
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Residues in contact with ALA 877 (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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568A ASN* 3.3 3.7 + - - +
571A LEU* 3.5 23.8 - - + -
863A PHE* 4.0 13.5 - - + -
873A LYS 3.3 2.6 + - - -
874A GLY 3.0 9.5 + - - +
876A VAL* 1.3 77.8 - - - +
878A CYS* 1.3 63.4 + - - +
880A ILE* 2.9 25.0 + - - +
885A GLU* 3.8 17.6 - - + +
886A LEU* 5.5 0.2 - - - -
889A THR* 3.5 22.1 - - + +
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Residues in contact with CYS 878 (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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233A ARG* 5.6 0.3 + - - -
238A ARG* 4.5 3.1 + - - -
568A ASN* 3.0 16.2 + - - +
571A LEU* 3.8 3.8 - - - -
572A ASN* 3.2 58.4 + - - +
575A ARG* 4.1 6.7 - - - +
870A ILE* 3.7 17.3 - - - -
874A GLY 2.9 17.9 + - - -
875A ARG* 3.4 14.4 - - - +
876A VAL 3.2 0.4 - - - -
877A ALA* 1.3 74.9 - - - +
879A GLU* 1.3 57.6 + - - +
880A ILE 3.4 0.2 - - - -
670B ILE* 4.2 16.6 - - + +
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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