Contacts of the helix formed by residues 882 - 893 (chain A) in PDB entry 3DPK
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 PRO 882 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SO4 3.8 11.9 - - - +
699A SER* 6.0 6.7 - - - -
756A LEU* 5.3 9.2 - - + -
849A PHE* 4.1 8.3 - - + -
877A GLN* 4.0 0.3 + - - -
880A PHE 3.3 11.0 - - - +
881A ALA* 1.3 88.1 - - - +
883A LYS* 1.3 65.8 + - - +
884A ASN* 4.3 7.0 - - + +
885A ILE* 3.0 35.7 + - + +
886A TYR 3.1 8.3 + - - -
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Residues in contact with LYS 883 (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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3A SO4 3.2 30.0 + - - +
877A GLN* 3.7 17.9 - - - +
882A PRO* 1.3 73.1 - - - +
884A ASN* 1.3 64.5 + - - +
886A TYR* 3.2 10.0 + - + +
887A SER* 3.0 38.4 + - - +
890A GLN* 4.9 7.5 + - - -
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Residues in contact with ASN 884 (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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882A PRO* 3.2 5.2 - - + +
883A LYS* 1.3 85.2 - - - +
885A ILE* 1.3 66.3 + - + +
887A SER* 3.3 17.0 + - - -
888A ILE* 3.4 16.5 + - - +
909A PHE* 3.6 25.0 - - + -
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Residues in contact with ILE 885 (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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756A LEU* 3.4 32.5 - - + -
845A LEU* 4.5 10.1 - - + -
849A PHE* 3.4 34.8 - - + -
881A ALA* 4.5 0.7 - - + -
882A PRO* 3.0 31.5 + - + +
884A ASN* 1.3 78.5 - - + +
886A TYR* 1.3 67.0 + - - +
888A ILE* 3.0 20.8 + - + +
889A MET* 3.2 20.8 + - + +
909A PHE* 5.8 1.1 - - + -
910A LEU* 3.9 20.9 - - + -
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Residues in contact with TYR 886 (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 GLN* 4.7 6.4 + - - +
875A MET 2.8 25.1 + - - -
876A ALA* 3.8 3.5 - - - -
877A GLN* 3.4 61.7 + - + -
878A PRO* 4.1 0.7 - - + -
881A ALA* 4.6 2.4 - - + +
882A PRO 3.1 9.1 + - - +
883A LYS* 3.2 15.9 + - + +
885A ILE* 1.3 77.1 - - - +
887A SER* 1.3 57.1 + - - +
889A MET* 3.2 24.1 + - - +
890A GLN* 3.0 59.8 + - + +
893A TRP* 4.2 13.9 - + - -
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Residues in contact with SER 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A LYS* 3.0 34.6 + - - +
884A ASN* 3.5 14.9 + - - -
885A ILE 3.1 0.2 - - - -
886A TYR* 1.3 78.2 - - - +
888A ILE* 1.3 62.0 + - - +
890A GLN* 3.4 14.3 + - - +
891A ALA* 3.1 23.7 + - - +
909A PHE* 5.4 5.2 - - - -
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Residues in contact with ILE 888 (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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845A LEU* 3.7 20.6 - - + -
884A ASN 3.5 9.6 - - - +
885A ILE* 3.0 19.7 + - + +
887A SER* 1.3 75.5 - - - +
889A MET* 1.3 66.5 + - - +
891A ALA* 3.1 7.2 + - - +
892A CYS* 2.9 32.8 + - - -
901A PRO* 5.6 2.0 - - + -
906A ILE* 4.4 24.5 - - + +
909A PHE* 3.7 29.4 - - + -
910A LEU* 3.5 35.4 - - + -
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Residues in contact with MET 889 (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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842A GLY* 3.8 15.7 - - - +
845A LEU* 3.8 32.8 - - + +
846A TRP* 3.8 27.1 - - - -
849A PHE* 4.3 0.7 - - + -
878A PRO* 3.9 18.4 - - + -
881A ALA* 4.1 8.1 - - + -
885A ILE* 3.2 27.3 + - + +
886A TYR* 3.2 23.9 + - + +
888A ILE* 1.3 76.3 - - - +
890A GLN* 1.3 63.8 + - - +
892A CYS* 3.0 8.4 + - - +
893A TRP* 3.0 47.5 + - + -
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Residues in contact with GLN 890 (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 GLN* 3.6 29.0 + - - +
883A LYS* 4.9 6.8 + - - -
886A TYR* 3.0 52.4 + - + +
887A SER* 3.7 23.2 + - - +
888A ILE 3.3 0.4 - - - -
889A MET* 1.3 76.1 - - - +
891A ALA* 1.3 61.9 + - - +
893A TRP* 3.1 15.1 + - + +
894A ALA* 3.4 9.9 + - - -
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Residues in contact with ALA 891 (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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887A SER 3.1 14.4 + - - +
888A ILE* 3.1 11.0 + - + +
890A GLN* 1.3 77.8 - - - +
892A CYS* 1.3 60.6 + - - +
893A TRP 3.2 0.9 + - - -
894A ALA* 3.2 20.3 + - - +
899A HIS 4.4 2.2 - - - +
900A ARG* 3.7 2.9 - - - +
901A PRO* 3.5 28.5 - - + +
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Residues in contact with CYS 892 (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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838A VAL* 3.4 40.8 - - - +
839A TRP* 3.4 11.1 - - - -
841A TYR* 4.2 2.9 - - - -
842A GLY* 3.8 20.9 - - - -
888A ILE* 2.9 25.5 + - - -
889A MET 3.4 8.3 - - - +
891A ALA* 1.3 76.5 - - - +
893A TRP* 1.3 59.6 + - + +
894A ALA 3.4 0.2 - - - -
900A ARG* 2.9 24.7 + - - -
901A PRO* 4.2 2.7 - - - -
906A ILE* 4.0 18.6 - - - -
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Residues in contact with TRP 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A TRP* 3.1 58.6 + + + -
842A GLY* 3.4 23.1 - - - -
843A ILE* 3.3 32.3 - - + +
846A TRP* 4.2 14.1 - + + -
856A TYR* 6.0 0.9 - - - -
874A GLN* 3.6 46.5 + - + +
875A MET* 4.0 30.7 - - + -
886A TYR* 4.2 8.1 - + - -
889A MET* 3.0 42.5 + - + +
890A GLN* 3.5 7.2 - - - +
891A ALA 3.1 0.8 - - - -
892A CYS* 1.3 79.2 - - + +
894A ALA* 1.3 65.1 + - - +
895A LEU* 3.3 5.0 + - - +
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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