Contacts of the helix formed by residues 991 - 1002 (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 CYS 991 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982A ARG* 4.0 17.7 - - - +
989A LEU 3.9 0.4 - - - -
990A SER* 1.3 81.3 - - - +
992A SER* 1.3 67.4 + - - +
993A LYS* 3.7 26.2 - - - -
994A ASP* 2.8 46.0 + - - +
995A ILE* 3.5 11.3 + - - +
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Residues in contact with SER 992 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982A ARG* 3.9 17.3 - - - +
991A CYS* 1.3 74.2 - - - +
993A LYS* 1.4 60.6 + - - +
995A ILE* 3.5 7.2 + - - +
996A GLN* 2.9 28.5 + - - +
999A LYS* 5.8 0.9 + - - -
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Residues in contact with LYS 993 (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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927A ARG* 5.0 16.2 - - + -
991A CYS* 3.4 17.1 - - - -
992A SER* 1.4 79.2 + - - +
994A ASP* 1.4 65.5 + - - +
996A GLN* 3.4 12.0 - - + +
997A TYR* 3.1 22.0 + - - +
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Residues in contact with ASP 994 (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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916A LEU* 3.5 25.0 - - + +
918A ASN* 4.7 7.4 - - - +
927A ARG* 5.4 5.2 - - - +
987A PRO 4.2 1.4 - - - +
988A GLU* 3.3 25.9 - - - +
989A LEU* 4.2 7.6 - - + -
990A SER* 2.8 29.8 + - - -
991A CYS* 2.8 28.6 + - - +
993A LYS* 1.4 79.0 - - - +
995A ILE* 1.4 60.5 + - - +
997A TYR* 3.1 26.2 - - - +
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Residues in contact with ILE 995 (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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916A LEU* 5.7 0.2 - - - -
975A LEU* 3.4 34.1 - - + +
978A PHE* 4.1 9.2 - - + -
979A ALA* 4.0 31.9 - - + +
982A ARG* 4.2 9.0 - - - +
989A LEU* 4.1 13.9 - - + -
991A CYS 3.5 8.8 + - - +
992A SER* 3.8 8.7 - - - +
994A ASP* 1.4 72.3 - - - +
996A GLN* 1.3 65.4 + - - +
998A LEU* 3.1 26.1 + - - +
999A LYS* 4.3 11.9 - - - +
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Residues in contact with GLN 996 (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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992A SER 2.9 19.7 + - - +
993A LYS* 3.4 14.1 - - + +
995A ILE* 1.3 73.4 - - - +
997A TYR* 1.4 66.6 + - - +
999A LYS* 2.9 48.0 + - - +
1000A ASP* 3.1 43.7 + - - +
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Residues in contact with TYR 997 (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 TYR 4.1 2.7 + - - -
888A VAL 4.1 2.5 - - - -
890A GLY* 3.3 35.4 - - - -
916A LEU* 3.3 34.3 - - + +
917A GLY* 3.5 18.2 - - - -
927A ARG* 6.0 1.1 - - + -
928A GLU 4.3 1.3 - - - -
929A ARG* 4.1 23.6 - - + +
930A VAL* 3.3 28.6 + - - +
993A LYS 3.1 11.9 + - - +
994A ASP* 3.1 17.7 + - - +
996A GLN* 1.4 77.6 - - - +
998A LEU* 1.3 50.8 + - - +
1000A ASP* 3.2 7.7 + - - +
1001A SER* 2.8 51.9 + - - -
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Residues in contact with LEU 998 (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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888A VAL* 3.5 34.3 - - + +
889A LEU* 4.6 9.9 - - + -
916A LEU* 4.0 15.5 - - + -
974A PHE* 3.7 23.3 - - + +
975A LEU* 3.7 11.7 - - + -
978A PHE* 3.4 41.7 - - + -
994A ASP 5.0 0.7 - - - +
995A ILE* 3.1 12.9 + - - +
997A TYR* 1.3 74.5 - - - +
999A LYS* 1.3 59.0 + - - +
1001A SER* 3.5 6.1 + - - +
1002A LEU* 3.0 41.6 + - + +
1004A LEU* 4.5 0.2 - - - +
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Residues in contact with LYS 999 (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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975A LEU* 3.8 36.3 - - + +
992A SER 5.8 0.6 + - - -
995A ILE* 3.5 17.8 + - - +
996A GLN* 2.9 44.8 + - - +
998A LEU* 1.3 73.5 - - - +
1000A ASP* 1.3 59.9 + - - +
1003A ALA* 3.0 6.4 + - - -
1004A LEU* 2.8 45.9 + - + +
1005A GLY 4.5 2.3 + - - +
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Residues in contact with ASP1000 (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 TYR* 5.2 0.9 + - - -
929A ARG* 5.4 13.8 - - + -
996A GLN* 3.1 37.7 + - - +
997A TYR* 3.6 8.1 - - - +
999A LYS* 1.3 74.0 - - - +
1001A SER* 1.4 59.7 + - - +
1003A ALA* 2.8 25.6 + - - +
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Residues in contact with SER1001 (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 TYR* 3.6 21.1 + - - -
888A VAL* 2.7 45.4 + - - +
964A TYR* 2.7 31.7 + - - -
997A TYR* 2.8 33.7 + - - -
998A LEU* 3.5 8.3 + - - -
1000A ASP* 1.4 70.2 - - - +
1002A LEU* 1.3 54.2 + - - +
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Residues in contact with LEU1002 (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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888A VAL* 4.2 28.7 - - + -
964A TYR* 3.3 12.8 - - + +
967A LEU* 3.6 20.6 - - + +
968A ARG* 2.9 53.9 + - + +
971A GLY* 3.9 29.2 - - - +
974A PHE* 4.5 15.7 - - + -
975A LEU* 6.3 0.7 - - + -
998A LEU* 3.0 21.2 + - + +
1001A SER* 1.3 74.8 + - - +
1003A ALA* 1.4 64.1 + - - +
1004A LEU* 2.9 12.7 + - + +
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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