Contacts of the helix formed by residues 1250 - 1261 (chain J) in PDB entry 6XAV
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 ASP1250 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822J MET* 4.7 5.3 - - + +
833J GLU* 5.8 0.4 - - - +
838J ARG* 3.4 36.5 + - - +
842J ARG* 3.5 13.2 - - - +
1234J VAL* 4.0 25.4 - - + +
1238J GLN* 3.5 22.6 + - - +
1248J ILE 3.8 0.9 - - - +
1249J ASN* 1.3 85.3 + - - +
1251J LYS* 1.3 61.8 + - - +
1252J HIS 3.1 4.0 + - - -
1253J ILE* 3.4 6.2 + - - +
1254J GLU* 3.3 28.1 + - - +
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Residues in contact with LYS1251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840J LEU 5.4 2.7 + - - -
841J GLY* 3.9 8.7 + - - -
842J ARG* 3.2 28.9 - - - +
885J VAL* 4.5 2.3 - - + +
899J TYR* 3.5 43.9 + - + +
900J GLY 3.9 0.2 - - - -
901J ARG* 2.8 44.7 + - - +
903J LEU* 4.2 13.6 - - + +
1249J ASN* 3.0 21.9 + - - +
1250J ASP* 1.3 75.2 - - - +
1252J HIS* 1.3 78.0 + - + +
1254J GLU* 4.1 7.1 - - - +
1255J VAL* 3.2 28.6 + - - +
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Residues in contact with HIS1252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493J PRO 2.9 27.1 + - - -
494J ALA* 3.7 10.5 - - - -
899J TYR* 3.5 22.9 + - - -
903J LEU* 3.4 20.0 - - + +
918J ILE* 4.8 9.4 - - + -
919J ALA* 3.7 30.1 - - + +
922J SER* 3.4 25.8 + - - -
923J ILE* 4.3 9.9 - - + -
1248J ILE* 4.5 9.2 - - + -
1249J ASN* 4.3 8.3 + - + +
1250J ASP 3.1 1.0 - - - -
1251J LYS* 1.3 84.6 + - + +
1253J ILE* 1.3 63.8 + - - +
1255J VAL* 3.3 11.6 + - - +
1256J ILE* 3.3 18.5 + - - +
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Residues in contact with ILE1253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923J ILE* 4.2 20.9 - - + -
1145J PHE* 4.4 19.5 - - + -
1233J ILE* 4.5 3.8 - - + +
1234J VAL* 3.9 30.5 - - + +
1237J VAL* 3.9 21.5 - - + -
1238J GLN* 3.7 37.7 - - + +
1241J TYR* 5.3 1.6 - - + -
1248J ILE* 5.4 2.5 - - + -
1249J ASN 4.4 9.6 - - - +
1250J ASP* 3.4 6.1 + - - +
1252J HIS* 1.3 75.0 - - + +
1254J GLU* 1.3 65.1 + - - +
1256J ILE* 3.1 4.2 + - - +
1257J VAL* 3.1 29.6 + - + +
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Residues in contact with GLU1254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820J ILE* 3.6 17.6 - - - +
822J MET* 5.4 5.9 - - - +
842J ARG* 3.5 32.7 + - - -
884J SER* 2.4 32.9 + - - +
885J VAL* 3.6 19.2 + - + +
886J VAL* 4.5 5.2 - - + +
1230J THR* 4.7 6.7 - - + -
1234J VAL* 4.1 18.3 - - + +
1250J ASP* 3.3 15.8 + - - +
1251J LYS* 4.2 2.8 - - - +
1252J HIS 3.3 0.6 - - - -
1253J ILE* 1.3 76.7 - - - +
1255J VAL* 1.3 61.8 + - - +
1257J VAL* 3.3 21.7 - - + +
1258J ARG* 3.3 12.0 + - - +
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Residues in contact with VAL1255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804J ALA* 5.0 2.2 - - + -
807J LEU* 3.6 21.8 - - + +
885J VAL* 4.0 21.5 - - + -
899J TYR* 4.0 19.7 - - + -
915J ILE* 4.3 7.6 - - + +
916J GLY* 4.1 12.8 - - - +
919J ALA* 4.1 18.2 - - + -
1251J LYS 3.2 16.8 + - - +
1252J HIS* 3.3 10.2 + - - +
1253J ILE 3.1 0.6 - - - -
1254J GLU* 1.3 76.2 - - - +
1256J ILE* 1.3 69.9 + - + +
1258J ARG* 3.3 18.4 + - - +
1259J GLN* 3.7 8.8 + - - +
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Residues in contact with ILE1256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800J LEU* 4.2 29.4 - - + +
803J VAL* 5.2 7.5 - - + +
804J ALA* 4.5 21.5 - - + -
919J ALA* 4.5 12.8 - - + -
920J ALA* 4.5 12.1 - - - +
923J ILE* 3.8 19.5 - - + -
1145J PHE* 4.7 13.9 - - + -
1252J HIS 3.3 15.0 + - - +
1253J ILE* 3.1 7.3 + - - +
1255J VAL* 1.3 78.0 - - - +
1257J VAL* 1.3 62.5 + - + +
1258J ARG 3.2 1.0 + - - -
1259J GLN* 3.3 14.6 + - - +
1260J MET* 3.3 25.6 + - + +
1309J ILE* 4.9 6.1 - - + -
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Residues in contact with VAL1257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886J VAL* 4.5 7.4 - - + -
1145J PHE* 5.3 1.1 - - + -
1230J THR* 4.3 24.2 - - + +
1233J ILE* 3.8 42.6 - - + -
1234J VAL* 5.6 0.9 - - + -
1253J ILE* 3.1 17.7 + - + +
1254J GLU* 3.3 22.4 - - - +
1256J ILE* 1.3 75.2 - - + +
1258J ARG* 1.3 64.7 + - - +
1260J MET* 3.2 24.4 + - - +
1261J LEU* 3.3 25.4 + - + +
1306J LEU* 6.4 0.2 - - + -
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Residues in contact with ARG1258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807J LEU* 4.4 12.0 - - - +
885J VAL* 2.7 45.1 + - - +
886J VAL* 4.4 15.1 + - + +
888J CYS* 3.7 20.6 + - - +
890J THR 3.2 25.7 + - - -
891J ASP* 5.2 0.6 - - - +
892J PHE 5.4 0.8 - - - +
893J GLY 3.4 12.9 + - - +
894J VAL* 3.5 15.3 - - - +
1254J GLU 3.3 14.4 + - - +
1255J VAL 3.3 11.2 + - - +
1256J ILE 3.1 0.4 - - - -
1257J VAL* 1.3 81.3 - - - +
1259J GLN* 1.3 75.3 + - - +
1260J MET 3.4 0.5 + - - -
1261J LEU* 3.5 10.8 + - + +
1262J ARG* 3.4 20.8 + - + +
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Residues in contact with GLN1259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803J VAL* 3.6 35.3 + - + +
804J ALA* 4.4 14.4 - - + +
806J ASP* 5.8 3.6 - - - +
807J LEU* 4.5 21.2 - - + +
1255J VAL 4.1 10.8 - - - +
1256J ILE* 3.3 7.9 + - - +
1258J ARG* 1.3 93.5 + - - +
1260J MET* 1.3 63.4 + - + +
1261J LEU 3.3 0.2 - - - -
1262J ARG* 3.0 57.8 - - - +
1312J ALA* 3.7 15.0 - - - +
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Residues in contact with MET1260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803J VAL* 6.2 2.7 - - + -
1144J LEU 4.4 7.9 - - - +
1145J PHE* 3.3 36.8 - - - +
1147J ALA* 4.5 7.4 - - + -
1233J ILE* 4.4 8.7 - - + -
1256J ILE* 3.3 23.3 - - + +
1257J VAL* 3.2 33.7 + - - +
1259J GLN* 1.3 79.6 - - - +
1261J LEU* 1.3 56.6 + - - +
1262J ARG 3.6 0.4 - - - -
1306J LEU* 3.7 23.8 - - + -
1307J LEU* 2.9 52.6 + - - +
1308J GLY 5.5 0.7 - - - -
1309J ILE* 5.0 8.1 - - + -
1312J ALA* 4.6 4.4 - - + +
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Residues in contact with LEU1261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886J VAL* 4.4 14.8 - - + +
1221J LEU* 4.4 20.0 - - + -
1226J VAL* 4.2 19.7 - - + -
1229J VAL* 4.4 10.1 - - + -
1230J THR* 5.0 4.5 - - - +
1233J ILE* 6.4 1.3 - - + -
1257J VAL* 3.3 25.1 + - + +
1258J ARG* 3.7 11.2 - - + +
1260J MET* 1.3 78.9 - - - +
1262J ARG* 1.3 51.0 + - - +
1263J LYS 3.1 10.7 + - - +
1304J ARG* 2.5 49.7 + - - +
1305J ASP 3.3 25.1 - - - +
1306J LEU* 4.5 11.2 - - + -
1307J LEU* 4.8 0.2 - - - -
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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