Contacts of the helix formed by residues 884 - 894 (chain A) in PDB entry 5EPG
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 LEU 884 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A PRO* 4.3 36.8 - - + +
720A GLU 5.8 0.2 - - - -
721A ARG* 3.8 36.6 - - + +
880A LEU* 3.8 23.3 - - + +
883A SER* 1.3 76.8 - - - +
885A PHE* 1.3 64.1 + - - +
886A VAL 3.2 0.4 - - - -
887A ILE* 3.2 12.6 + - + +
888A GLU* 3.1 35.6 + - - +
907A GLY 5.9 0.9 - - - +
909A ALA* 4.9 12.6 - - + +
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Residues in contact with PHE 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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883A SER 3.9 10.2 - - - +
884A LEU* 1.3 77.0 - - - +
886A VAL* 1.3 57.6 + - - +
888A GLU* 3.3 20.1 + - - +
889A MET* 3.0 35.3 + - + +
923A PHE* 4.0 23.1 - + + -
1019A GLY* 6.4 1.8 - - - -
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Residues in contact with VAL 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A HIS* 3.7 37.5 - - + +
851A TYR* 3.5 28.9 + - + +
874A SER* 4.6 2.7 - - - -
883A SER* 3.5 14.6 + - - +
884A LEU 3.2 0.6 - - - -
885A PHE* 1.3 77.7 - - - +
887A ILE* 1.3 62.8 + - - +
889A MET* 4.2 0.4 - - - +
890A GLY* 3.0 21.8 + - - -
919A ALA* 4.8 7.0 - - + -
920A PHE 5.8 0.4 - - - +
923A PHE* 3.5 32.3 - - + -
924A GLY* 4.0 18.2 - - - +
927A GLN* 5.1 1.1 - - - +
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Residues in contact with ILE 887 (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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721A ARG* 4.4 11.0 - - + -
851A TYR* 3.8 13.8 + - + +
872A HIS* 4.6 4.3 - - + +
873A TYR 4.6 0.4 - - - -
874A SER* 3.8 24.0 - - - +
883A SER 3.4 13.9 + - - +
884A LEU* 3.2 13.6 + - + +
886A VAL* 1.3 76.0 - - - +
888A GLU* 1.3 58.1 + - - +
890A GLY* 3.2 1.6 + - - -
891A LEU* 2.9 37.4 + - + +
907A GLY* 3.7 29.2 - - - +
908A TRP 3.6 31.0 - - - +
909A ALA* 4.1 13.0 - - + +
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Residues in contact with GLU 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A ARG* 2.9 54.7 + - + +
884A LEU* 3.1 27.0 + - - +
885A PHE* 3.3 23.3 + - + +
887A ILE* 1.3 75.3 - - - +
889A MET* 1.3 63.0 + - + +
891A LEU* 3.3 2.0 + - - +
892A LEU* 3.1 33.3 + - + +
1151A TRP* 3.6 31.6 + - + +
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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
----------------------------------------------------------
885A PHE* 3.0 21.2 + - + +
886A VAL 4.3 0.2 - - - +
888A GLU* 1.3 73.1 - - + +
890A GLY* 1.3 65.6 + - - +
892A LEU* 4.2 17.0 - - - -
893A LYS* 3.0 60.0 + - - +
923A PHE* 3.3 39.0 - - + +
924A GLY 5.2 0.2 - - - -
1017A GLY 3.4 25.8 - - - +
1018A LEU* 5.2 6.7 - - + -
1159A PHE* 4.2 10.5 - - + -
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Residues in contact with GLY 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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851A TYR* 4.2 6.1 - - - -
872A HIS* 4.3 3.6 - - - -
886A VAL 3.0 16.7 + - - -
887A ILE 3.2 4.6 + - - -
889A MET* 1.3 77.0 - - - +
891A LEU* 1.3 56.1 + - - +
893A LYS* 3.6 0.4 - - - -
894A MET* 2.9 31.2 + - - +
923A PHE 4.4 0.8 + - - -
924A GLY 4.0 8.5 - - - -
928A ALA* 3.3 24.7 - - - +
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Residues in contact with LEU 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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721A ARG* 3.6 43.3 - - + +
722A LYS* 3.9 6.7 - - - +
723A LEU* 3.1 22.7 - - + +
872A HIS* 3.6 16.8 - - + +
887A ILE* 2.9 21.6 + - + +
888A GLU 3.8 4.3 - - - +
889A MET 3.3 0.2 - - - -
890A GLY* 1.3 75.3 - - - +
892A LEU* 1.3 61.6 + - - +
893A LYS 3.5 0.2 + - - -
894A MET* 3.5 21.3 + - - +
895A ASP* 5.0 0.7 - - - +
905A CYS* 3.4 29.2 - - - +
906A ARG 4.2 0.4 - - - -
907A GLY* 4.1 17.3 - - - +
963A PRO* 6.1 0.2 - - - +
1151A TRP* 3.7 18.2 - - + -
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Residues in contact with LEU 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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723A LEU* 4.2 4.3 - - + -
888A GLU* 3.1 25.8 + - + +
889A MET* 4.0 14.4 - - - +
890A GLY 3.3 0.2 - - - -
891A LEU* 1.3 76.2 - - - +
893A LYS* 1.3 58.8 + - - +
895A ASP* 2.9 19.9 - - - +
964A TYR* 3.0 35.3 + - + -
1015A PRO* 4.9 0.3 - - - +
1149A MET* 3.7 37.0 - - + -
1151A TRP* 3.8 19.5 - - + +
1158A PRO* 4.5 10.1 - - + -
1159A PHE* 3.8 26.3 - - + -
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Residues in contact with LYS 893 (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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889A MET* 3.0 55.3 + - + +
890A GLY 3.6 1.8 - - - +
892A LEU* 1.3 76.2 - - - +
894A MET* 1.3 62.8 + - - +
895A ASP* 3.4 4.0 - - - -
896A ASN* 3.2 12.5 + - - +
922A GLY 4.0 9.1 + - - +
923A PHE* 4.6 3.6 + - - +
925A PHE* 3.7 38.4 - - + -
928A ALA* 5.0 0.7 - - - -
929A ALA* 5.0 0.9 - - - +
1013A LYS* 4.9 0.9 - - - +
1014A PHE* 3.7 29.4 - - + -
1015A PRO* 3.3 47.4 + - + -
1016A VAL* 5.7 0.2 - - - +
1159A PHE* 4.0 11.9 - - + -
1270A GLU* 5.6 1.2 + - - -
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Residues in contact with MET 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A LEU* 5.7 0.2 - - + -
868A LEU* 5.9 0.9 - - + -
870A MET* 4.4 9.9 - - + -
872A HIS* 3.8 21.3 - - + +
890A GLY 2.9 16.9 + - - +
891A LEU 3.5 11.9 - - - +
892A LEU 3.4 1.8 - - - -
893A LYS* 1.3 77.0 - - - +
895A ASP* 1.3 86.8 + - + +
896A ASN* 3.2 2.4 + - - +
900A PHE* 5.5 4.9 - - + -
903A LEU* 3.7 33.7 - - + -
905A CYS* 3.4 31.4 - - + -
928A ALA* 4.3 9.3 - - - +
929A ALA* 4.7 0.7 - - - -
932A THR* 3.0 44.5 + - + +
963A PRO* 5.0 1.6 - - + -
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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