Contacts of the helix formed by residues 884 - 893 (chain A) in PDB entry 6V3O
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 ASP 884 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A GLY 4.8 4.7 - - - +
136A SER* 4.2 23.9 + - - -
651A PRO* 6.1 0.3 - - - +
881A LEU* 3.1 30.5 + - + +
883A GLY* 1.3 78.8 - - - +
885A PRO* 1.3 65.1 - - - +
886A PHE* 3.6 10.1 + - - +
887A LEU* 3.1 35.6 + - - +
888A LYS* 3.1 17.8 + - - +
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Residues in contact with PRO 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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28A VAL* 4.3 16.5 - - + +
126A LEU* 6.3 0.9 - - + -
881A LEU 4.0 2.6 - - - +
882A GLU 4.3 7.9 - - - +
883A GLY 3.6 7.6 - - - +
884A ASP* 1.3 89.5 - - - +
886A PHE* 1.3 73.4 + - + +
888A LYS* 3.7 7.2 - - + +
889A GLN* 2.8 32.4 + - - +
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Residues in contact with PHE 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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28A VAL* 3.5 36.6 - - + -
29A SER* 4.4 14.4 - - - -
120A ARG* 3.5 40.8 + - - +
126A LEU* 3.9 29.8 - - + -
136A SER* 5.2 0.7 - - - +
138A THR* 3.4 42.6 - - + -
884A ASP* 3.2 7.5 - - - +
885A PRO* 1.3 89.7 - - + +
887A LEU* 1.3 62.9 + - - +
889A GLN* 3.4 7.1 + - - +
890A GLY* 3.1 18.2 + - - -
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Residues in contact with LEU 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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113A GLU* 5.9 2.5 - - - +
647A ARG* 4.9 2.0 - - - +
679A PHE* 6.5 0.2 - - + -
831A MET* 4.2 18.8 - - + -
881A LEU* 3.7 28.9 - - + -
884A ASP* 3.1 28.2 + - - +
886A PHE* 1.3 73.2 - - - +
888A LYS* 1.3 66.4 + - - +
890A GLY* 3.0 3.5 + - - +
891A LEU* 3.0 59.4 + - + +
1004A FLC 3.6 39.0 - - + +
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Residues in contact with LYS 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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834A ALA* 4.5 8.5 - - + +
879A ASP* 5.4 5.3 + - - +
880A ILE* 3.5 42.9 + - + +
881A LEU* 3.8 26.6 - - + +
884A ASP 3.1 17.6 + - - +
885A PRO* 3.8 7.6 - - + +
887A LEU* 1.3 78.1 - - - +
889A GLN* 1.3 59.4 + - - +
891A LEU* 3.4 2.1 + - + +
892A VAL* 2.9 49.8 + - + +
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Residues in contact with GLN 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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24A VAL* 4.2 25.5 - - + +
26A GLY 4.7 7.1 + - - -
28A VAL* 3.4 22.5 - - + +
32A ASP* 3.0 38.3 + - - +
34A LEU* 4.2 20.7 - - + +
35A ILE* 4.7 9.5 - - - +
120A ARG* 5.0 6.1 + - - -
885A PRO 2.8 18.3 + - - +
886A PHE* 3.7 5.7 - - - +
888A LYS* 1.3 78.9 - - - +
890A GLY* 1.3 61.5 + - - +
891A LEU 3.3 0.5 + - - -
892A VAL* 3.6 0.7 + - - +
893A LEU* 3.2 43.2 + - + +
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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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34A LEU* 4.6 11.0 - - - -
113A GLU* 3.8 26.2 - - - +
886A PHE 3.1 10.9 + - - -
887A LEU* 3.0 8.4 + - - -
889A GLN* 1.3 78.2 + - - +
891A LEU* 1.3 64.5 + - - +
893A LEU* 4.0 4.7 + - - +
894A ARG* 3.3 21.9 + - - +
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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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113A GLU* 5.4 0.4 - - - +
831A MET* 4.4 3.1 - - + +
834A ALA* 4.1 13.9 - - + +
835A LYS* 4.1 31.2 - - + -
881A LEU* 4.1 15.5 - - + -
887A LEU* 3.0 37.6 + - + +
888A LYS* 4.1 2.9 - - + +
889A GLN 3.2 0.2 - - - -
890A GLY* 1.3 75.8 - - - +
892A VAL* 1.3 67.7 + - + +
893A LEU 3.2 1.8 - - - -
894A ARG* 3.0 40.7 + - - +
895A ASN* 3.5 12.0 + - - +
1004A FLC 3.3 27.4 - - - +
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Residues in contact with VAL 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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23A LEU* 4.4 31.1 - - + +
24A VAL* 4.7 10.3 - - + -
72A GLU* 4.8 5.6 - - + +
834A ALA 6.1 1.1 - - - +
888A LYS* 2.9 45.4 + - + +
889A GLN* 3.6 2.9 + - - +
891A LEU* 1.3 76.9 - - + +
893A LEU* 1.3 62.3 + - - +
894A ARG 3.1 0.2 - - - -
895A ASN* 3.2 30.1 + - - +
896A PRO* 3.4 10.6 - - - +
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Residues in contact with LEU 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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20A LEU* 3.6 48.3 - - + +
23A LEU* 4.5 4.9 - - + -
24A VAL* 4.2 12.3 - - + -
34A LEU* 4.0 20.9 - - + -
35A ILE* 4.2 13.7 - - + -
38A ASP* 4.1 17.6 - - - +
109A ALA* 4.8 1.9 - - - +
889A GLN* 3.2 43.8 + - + +
890A GLY* 4.0 3.6 + - - +
891A LEU 3.2 1.2 - - - -
892A VAL* 1.3 76.3 - - - +
894A ARG* 1.3 58.8 + - - +
896A PRO* 3.9 7.1 - - - +
897A TYR* 3.4 21.5 + - - -
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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