Contacts of the helix formed by residues 970 - 982 (chain A) in PDB entry 5VLR
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 HIS 970 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577A LEU* 6.5 0.4 - - - -
800A LEU* 3.5 54.6 - - + +
803A GLN* 5.3 4.4 + - - -
804A GLU* 6.1 5.2 - - + -
966A ILE* 3.4 19.9 + - + -
967A LEU 3.3 10.3 + - - +
968A ARG 3.1 0.4 - - - -
969A ARG* 1.4 85.1 - - + +
971A GLY* 1.3 59.9 + - - +
972A LEU 3.4 2.7 - - - -
973A LEU* 3.2 26.8 + - + +
974A PHE* 3.0 17.4 - - + -
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Residues in contact with GLY 971 (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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967A LEU 3.2 6.8 + - - -
968A ARG 2.9 15.8 + - - -
969A ARG 3.5 1.2 + - - -
970A HIS* 1.3 76.3 - - - +
972A LEU* 1.3 61.9 + - - +
974A PHE* 3.4 5.1 + - - +
975A LEU* 3.1 30.9 + - - +
1002A LEU* 3.9 17.5 - - - +
1004A LEU* 4.4 10.5 - - - -
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Residues in contact with LEU 972 (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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577A LEU* 4.0 24.2 - - + -
969A ARG 5.4 0.4 + - - -
970A HIS 3.4 0.6 - - - -
971A GLY* 1.3 72.6 - - - +
973A LEU* 1.4 55.5 + - - +
975A LEU* 3.3 17.7 + - + +
976A HIS* 2.9 63.5 + - + +
1004A LEU* 5.3 1.1 - - + +
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Residues in contact with LEU 973 (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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576A VAL* 5.9 0.4 - - + -
577A LEU* 3.5 21.2 - - + +
580A LEU* 3.8 26.0 - - + -
611A TYR* 3.7 31.0 - - + +
796A LEU* 4.2 22.9 - - + -
800A LEU* 4.6 10.8 - - + -
970A HIS* 3.2 32.8 + - + +
972A LEU* 1.4 77.7 - - - +
974A PHE* 1.3 53.0 + - + +
976A HIS* 3.4 1.8 + - - +
977A LEU* 2.8 47.7 + - + +
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Residues in contact with PHE 974 (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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793A MET* 4.0 24.5 - - + -
796A LEU* 4.1 17.9 - - + -
797A MET* 3.8 38.4 - - + -
800A LEU* 3.5 33.9 - - + -
888A VAL* 5.9 2.0 - - + -
889A LEU* 5.4 1.8 - - + -
967A LEU* 4.0 21.3 - - + -
970A HIS* 3.0 25.1 + - + -
971A GLY* 3.4 7.7 + - - +
972A LEU 3.4 0.4 - - - -
973A LEU* 1.3 76.2 - - + +
975A LEU* 1.3 59.6 + - + +
977A LEU* 4.5 5.2 - - - -
978A PHE* 3.0 41.1 + + + +
998A LEU* 4.1 16.4 - - + -
1002A LEU* 4.5 10.5 - - + -
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Residues in contact with LEU 975 (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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971A GLY 3.1 21.3 + - - +
972A LEU* 3.3 22.6 + - + +
974A PHE* 1.3 75.1 - - - +
976A HIS* 1.4 58.6 + - - +
978A PHE* 3.7 2.9 - - - +
979A ALA* 2.8 37.8 + - - +
995A ILE* 3.4 40.6 - - + +
998A LEU* 3.7 18.2 - - + -
999A LYS* 3.8 34.8 - - + +
1002A LEU* 6.3 0.4 - - + -
1004A LEU* 4.1 13.2 - - + -
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Residues in contact with HIS 976 (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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577A LEU* 3.0 45.9 + - + +
578A SER* 5.0 1.6 - - - -
580A LEU* 4.3 16.4 - - + -
581A GLU* 3.6 44.7 + - + +
972A LEU* 2.9 44.2 + - + +
973A LEU* 3.6 5.4 - - - +
975A LEU* 1.4 76.7 - - - +
977A LEU* 1.4 61.6 + - - +
979A ALA* 3.3 8.2 + - - +
980A LEU* 3.1 29.3 + - - +
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Residues in contact with LEU 977 (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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580A LEU* 4.2 18.6 - - + -
610A GLN 4.9 0.2 - - - +
611A TYR* 3.6 40.8 - - + -
614A GLN* 3.3 35.1 - - + +
792A GLN* 4.7 2.5 - - - +
793A MET* 3.8 23.1 - - + -
796A LEU* 3.6 31.4 - - + -
973A LEU* 2.8 31.3 + - + +
974A PHE* 4.1 2.2 - - - +
976A HIS* 1.4 72.1 - - - +
978A PHE* 1.3 61.3 + - - +
980A LEU* 3.1 5.9 + - + +
981A MET* 3.1 17.9 + - - +
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Residues in contact with PHE 978 (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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789A LEU* 4.4 3.8 - - + -
793A MET* 3.5 38.4 - - + -
889A LEU* 3.8 25.4 - - + -
915A PHE* 3.6 34.3 - + - -
916A LEU* 4.0 15.5 - - + -
974A PHE* 3.0 30.5 + + - +
975A LEU* 3.9 3.1 - - - +
977A LEU* 1.3 71.6 - - - +
979A ALA* 1.4 64.9 + - - +
981A MET* 3.0 21.1 + - - +
982A ARG 3.4 5.4 + - - -
989A LEU* 3.4 34.4 - - + +
995A ILE* 4.1 12.8 - - + -
998A LEU* 3.4 23.8 - - + -
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Residues in contact with ALA 979 (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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584A ASP* 3.6 26.7 - - - +
585A PHE* 5.8 0.3 - - - -
975A LEU 2.8 23.0 + - - +
976A HIS* 3.5 9.0 - - - +
977A LEU 3.3 0.2 - - - -
978A PHE* 1.4 71.3 - - - +
980A LEU* 1.3 60.6 + - + +
982A ARG* 3.3 28.1 - - - +
995A ILE* 4.0 16.8 - - + +
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Residues in contact with LEU 980 (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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580A LEU* 3.6 36.6 - - + +
581A GLU* 5.4 1.1 - - - -
583A LEU* 4.1 13.9 - - + -
584A ASP* 3.7 38.1 - - + +
614A GLN* 4.1 22.7 - - + -
615A LEU 5.1 0.7 - - - +
617A GLN* 4.4 4.4 - - - +
618A VAL* 3.7 29.2 - - + +
621A TYR* 4.4 1.1 + - - -
976A HIS 3.1 20.8 + - - +
977A LEU* 3.1 8.2 + - + +
979A ALA* 1.3 70.4 - - - +
981A MET* 1.4 59.0 + - - +
982A ARG 3.0 10.3 + - - -
983A ALA* 3.1 22.5 + - - +
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Residues in contact with MET 981 (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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613A LEU* 4.0 23.3 - - + -
614A GLN* 3.5 35.2 - - + +
617A GLN* 3.7 22.0 - - + -
785A ARG* 5.6 4.3 - - + +
789A LEU* 3.8 29.2 - - + -
977A LEU 3.1 7.8 + - - +
978A PHE* 3.0 7.5 + - - +
980A LEU* 1.4 69.2 - - - +
982A ARG* 1.3 55.6 + - - +
983A ALA 3.0 5.4 - - - -
984A ALA* 3.0 49.2 + - + +
985A GLY 4.2 1.0 + - - -
986A LEU* 4.1 7.8 - - + +
989A LEU* 3.4 29.1 - - + +
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Residues in contact with ARG 982 (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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584A ASP* 5.7 1.8 + - - -
585A PHE* 4.0 30.6 - - + -
621A TYR* 3.6 10.4 + - - +
978A PHE 3.4 6.7 + - - +
979A ALA* 3.3 29.2 - - - +
980A LEU 3.0 0.8 + - - -
981A MET* 1.3 77.8 - - - +
983A ALA* 1.4 57.3 + - - +
984A ALA 3.5 0.5 + - - -
985A GLY* 3.5 12.7 + - - -
989A LEU* 3.8 28.5 - - + +
990A SER* 4.0 13.3 + - - +
991A CYS* 4.0 24.2 - - - +
992A SER* 3.9 19.2 - - - +
995A ILE* 4.2 12.6 - - - +
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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