Contacts of the helix formed by residues 869 - 879 (chain A) in PDB entry 3MP6
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 869 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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864A PRO* 3.4 13.4 - - + +
865A LYS* 3.1 30.2 + - - +
866A THR* 3.1 31.1 + - - +
867A TRP 3.1 0.8 + - - -
868A GLU* 1.3 76.0 - - + +
870A ILE* 1.3 64.8 + - - +
871A PRO 3.5 1.1 - - - -
872A ALA* 3.5 8.0 + - - +
873A LEU* 3.2 21.9 + - + +
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Residues in contact with ILE 870 (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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853A LEU* 6.0 0.4 - - + -
864A PRO* 4.2 5.6 - - + -
866A THR 3.9 8.1 - - - +
867A TRP* 2.9 48.2 + - + +
869A GLU* 1.3 75.6 - - - +
871A PRO* 1.3 69.6 - - + +
873A LEU* 3.2 5.3 + - - +
874A ASP* 2.9 23.5 + - + +
884A ALA* 4.1 17.0 - - + -
885A LEU* 3.9 26.9 - - + -
936A LEU* 4.4 15.9 - - + -
941A HIS* 5.4 3.4 - - + -
942A MET* 6.4 0.9 - - + -
962A MET* 4.1 18.8 - - + -
986A PRO* 4.4 11.2 - - + -
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Residues in contact with PRO 871 (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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867A TRP 3.6 5.4 - - - +
868A GLU 3.3 17.3 - - - +
870A ILE* 1.3 93.5 - - + +
872A ALA* 1.3 59.8 + - - +
874A ASP* 3.2 2.8 + - - +
875A LYS* 3.0 36.5 + - - +
932A PHE* 4.2 9.4 - - + -
936A LEU* 3.9 19.7 - - + -
939A ASN* 6.3 0.9 - - - +
941A HIS* 3.8 26.2 - - + +
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Residues in contact with ALA 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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868A GLU 5.0 1.5 + - - +
869A GLU* 3.5 9.5 + - - +
870A ILE 3.3 0.6 - - - -
871A PRO* 1.3 79.2 - - - +
873A LEU* 1.3 63.0 + - - +
875A LYS* 3.2 16.8 + - + +
876A GLU* 3.1 22.4 + - - +
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Residues in contact with LEU 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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860A LEU* 3.7 28.0 - - + -
864A PRO* 3.8 31.2 - - + -
869A GLU 3.2 14.9 + - - +
870A ILE* 3.2 5.9 + - - +
872A ALA* 1.3 79.0 - - - +
874A ASP* 1.3 57.2 + - - +
876A GLU* 3.2 35.7 + - - +
877A LEU* 2.9 41.4 + - + +
884A ALA* 4.0 5.4 - - + -
962A MET* 3.8 20.2 - - + -
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Residues in contact with ASP 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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870A ILE* 2.9 16.1 + - + +
871A PRO 3.2 0.6 + - - +
873A LEU* 1.3 77.6 - - - +
875A LYS* 1.3 56.1 + - - +
877A LEU* 3.9 0.6 - - - +
878A LYS* 2.8 63.4 + - - +
883A SER* 3.3 13.3 - - - -
884A ALA* 2.9 37.1 + - + +
940A LYS 3.9 0.2 - - - +
941A HIS* 2.7 44.4 + - + +
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Residues in contact with LYS 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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871A PRO* 3.0 27.3 + - - +
872A ALA* 3.2 13.5 + - + +
874A ASP* 1.3 77.5 - - - +
876A GLU* 1.3 62.7 + - - +
878A LYS* 3.6 11.3 + - - +
879A ALA* 3.7 10.2 + - - +
941A HIS* 4.2 20.9 - - + -
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Residues in contact with GLU 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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859A LEU 5.2 2.8 - - - +
860A LEU* 5.2 2.3 - - - +
872A ALA 3.1 12.4 + - - +
873A LEU* 3.4 33.8 - - - +
875A LYS* 1.3 76.1 - - - +
877A LEU* 1.3 72.4 + - + +
879A ALA* 3.4 20.3 + - - +
880A LYS* 4.1 4.0 + - - +
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Residues in contact with LEU 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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859A LEU* 4.5 16.4 - - + +
860A LEU* 5.4 0.7 - - + -
873A LEU* 2.9 31.2 + - + +
874A ASP 4.0 2.2 - - - +
876A GLU* 1.3 87.7 - - + +
878A LYS* 1.3 60.8 + - - +
879A ALA 3.1 2.0 - - - -
880A LYS* 2.9 46.8 + - - +
882A LYS* 3.0 37.2 + - + +
883A SER 3.7 7.0 - - - +
884A ALA* 3.6 28.5 - - - -
961A ALA* 3.8 17.5 - - + -
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Residues in contact with LYS 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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874A ASP* 2.8 59.9 + - - +
875A LYS* 3.9 7.6 - - - +
876A GLU 3.4 0.4 - - - -
877A LEU* 1.3 75.4 - - - +
879A ALA* 1.3 58.1 + - - +
881A GLY* 2.9 20.1 + - - -
882A LYS 3.1 19.6 + - - +
883A SER* 3.7 13.1 - - - -
940A LYS 3.0 21.8 + - - -
941A HIS* 4.3 2.6 + - - +
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Residues in contact with ALA 879 (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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875A LYS 3.7 8.2 + - - +
876A GLU* 3.4 14.4 + - - +
877A LEU 3.1 0.6 - - - -
878A LYS* 1.3 77.8 - - - +
880A LYS* 1.3 58.8 + - + +
881A GLY 3.4 0.6 + - - -
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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