Contacts of the helix formed by residues 1237 - 1245 (chain J) in PDB entry 6PSS
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 VAL1237 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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923J ILE* 5.5 0.2 - - + -
1141J VAL* 3.8 13.7 - - + -
1144J LEU* 3.7 26.9 - - + -
1145J PHE* 4.2 15.0 - - + -
1233J ILE* 2.6 39.3 + - + +
1236J GLU* 1.3 73.2 - - - +
1238J GLN* 1.3 57.5 + - - +
1240J VAL* 2.9 20.4 + - - +
1241J TYR* 3.1 35.8 + - + -
1253J ILE* 3.8 24.7 - - + -
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Residues in contact with GLN1238 (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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833J GLU* 5.3 4.1 + - - +
838J ARG* 6.3 1.6 - - - +
1234J VAL 3.2 22.9 + - - +
1235J ASN* 4.1 1.3 + - - +
1236J GLU 3.4 0.2 - - - -
1237J VAL* 1.3 75.9 - - - +
1239J ASP* 1.3 58.2 + - - +
1240J VAL 3.2 0.2 - - - -
1241J TYR* 3.7 6.8 - - - +
1242J ARG* 2.9 69.8 + - - +
1246J VAL 5.2 0.2 - - - +
1247J LYS* 5.6 0.3 - - - -
1248J ILE* 2.7 46.5 + - + +
1249J ASN 4.0 0.4 - - - -
1250J ASP* 3.5 26.6 - - + +
1253J ILE* 3.6 14.1 - - + +
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Residues in contact with ASP1239 (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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825J VAL* 5.0 5.0 - - - +
1134J ILE* 5.3 4.0 - - + +
1135J THR 5.1 1.8 - - - +
1235J ASN* 3.1 24.7 + - - +
1236J GLU* 3.6 19.7 - - + +
1237J VAL 3.1 1.2 - - - -
1238J GLN* 1.3 77.1 - - - +
1240J VAL* 1.3 60.5 + - + +
1242J ARG* 3.1 22.0 + - - +
1243J LEU* 3.2 25.4 + - - +
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Residues in contact with VAL1240 (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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930J LEU* 4.1 7.1 - - + +
1135J THR 4.3 6.5 - - - +
1136J GLY* 4.1 5.6 - - - -
1137J GLY 3.3 39.3 - - - +
1140J ARG* 3.8 25.1 - - + -
1141J VAL* 3.7 15.7 - - + -
1144J LEU* 4.2 6.1 - - + -
1236J GLU 3.4 17.5 - - - +
1237J VAL 2.9 7.5 + - - +
1239J ASP* 1.3 81.1 - - + +
1241J TYR* 1.3 64.5 + - - +
1243J LEU* 3.6 10.2 + - - +
1244J GLN* 3.6 16.5 + - - -
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Residues in contact with TYR1241 (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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796J LEU* 4.8 2.3 - - - +
923J ILE* 2.8 38.9 + - + +
926J PRO* 4.0 6.3 - - + -
927J GLY* 3.4 30.1 - - - -
930J LEU* 3.7 17.1 - - + +
1138J LEU* 5.0 0.2 - - - +
1141J VAL* 4.0 15.9 - - + +
1237J VAL* 3.1 47.6 + - + +
1238J GLN* 3.5 7.1 + - - +
1240J VAL* 1.3 78.4 - - - +
1242J ARG* 1.3 58.3 + - - +
1244J GLN 3.5 2.3 + - - -
1245J GLY 3.1 7.6 + - - -
1246J VAL* 2.8 54.2 + - + +
1248J ILE* 4.0 28.9 - - + -
1253J ILE* 5.3 0.4 - - + -
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Residues in contact with ARG1242 (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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825J VAL* 3.7 28.1 - - - +
832J LYS* 5.1 11.0 - - + +
833J GLU* 3.8 38.1 + - - +
838J ARG* 4.1 5.9 - - - +
1235J ASN* 3.6 18.4 + - - -
1238J GLN* 2.9 46.8 + - - +
1239J ASP* 3.1 26.2 + - - -
1241J TYR* 1.3 76.0 - - - +
1243J LEU* 1.3 65.0 + - - +
1244J GLN 3.4 0.2 - - - -
1245J GLY* 3.4 12.6 + - - +
1246J VAL 4.2 7.2 - - - +
1247J LYS* 4.6 18.2 - - - +
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Residues in contact with LEU1243 (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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935J PHE* 4.2 18.8 - - + -
937J ILE* 5.1 8.7 - - + -
1134J ILE* 4.0 30.1 - - + +
1135J THR 4.2 2.2 - - - +
1136J GLY* 3.7 33.2 - - - +
1239J ASP 3.2 21.5 + - - +
1240J VAL 3.7 5.6 - - - +
1241J TYR 3.2 0.6 - - - -
1242J ARG* 1.3 80.4 - - - +
1244J GLN* 1.3 61.6 + - - +
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Residues in contact with GLN1244 (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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929J GLN 4.8 4.9 - - - +
930J LEU* 3.5 37.7 - - + +
931J THR* 2.5 32.7 + - - -
935J PHE* 3.3 19.5 - - - -
1136J GLY* 4.8 1.4 - - - -
1137J GLY 4.0 17.0 - - - +
1240J VAL 3.6 8.7 + - - -
1241J TYR 3.5 2.5 + - - +
1243J LEU* 1.3 81.0 - - - +
1245J GLY* 1.3 57.9 + - - +
1246J VAL* 4.2 6.2 - - + +
14N GLN* 5.7 0.5 - - - +
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Residues in contact with GLY1245 (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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1241J TYR 3.1 3.9 + - - -
1242J ARG* 3.4 10.0 + - - -
1243J LEU 3.3 3.0 - - - -
1244J GLN* 1.3 79.7 - - - +
1246J VAL* 1.3 63.3 + - - +
1247J LYS* 3.7 11.4 + - - +
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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