Contacts of the helix formed by residues 1138 - 1145 (chain J) in PDB entry 6PSU
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 LEU1138 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789J LYS* 6.1 4.9 - - + -
792J ASN 5.6 0.7 - - - +
795J TYR* 3.5 35.4 - - + +
796J LEU* 5.1 16.4 - - + -
927J GLY* 3.4 44.4 - - - +
928J THR* 5.7 0.7 - - + -
930J LEU* 3.5 13.2 - - + +
931J THR 3.0 17.1 + - - +
932J MET* 4.2 8.3 - - + +
1137J GLY* 1.3 69.6 - - - -
1139J PRO* 1.3 62.9 - - + +
1140J ARG 3.0 4.5 - - - -
1141J VAL* 2.4 41.3 + - + +
1142J ALA* 3.3 3.3 + - - +
1241J TYR* 5.0 2.5 - - - +
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Residues in contact with PRO1139 (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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795J TYR* 3.6 19.1 - - + +
932J MET* 2.9 28.7 - - + +
933J ARG* 5.3 0.4 - - - -
934J THR* 4.6 15.0 - - + +
1137J GLY 4.1 0.2 - - - -
1138J LEU* 1.3 86.2 - - + +
1140J ARG* 1.3 59.5 + - - +
1141J VAL 3.1 0.2 - - - -
1142J ALA* 4.0 8.4 - - + +
1143J ASP* 3.4 22.0 + - - +
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Residues in contact with ARG1140 (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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934J THR* 4.2 15.9 - - - +
1135J THR* 3.5 27.4 + - - +
1136J GLY 4.7 0.2 - - - +
1137J GLY* 3.7 24.0 - - - +
1138J LEU 3.0 0.2 - - - -
1139J PRO* 1.3 78.9 - - - +
1141J VAL* 1.3 57.4 + - - +
1143J ASP* 3.9 18.6 + - - +
1144J LEU* 3.0 44.0 + - + +
1150J PRO* 6.2 1.6 - - - +
1232J TYR* 4.9 5.9 + - - -
1236J GLU* 3.0 24.0 + - - -
1240J VAL* 4.6 12.1 - - + +
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Residues in contact with VAL1141 (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* 4.5 11.0 - - + -
923J ILE* 5.3 0.9 - - + -
930J LEU* 4.6 8.5 - - + -
1137J GLY 3.6 17.7 - - - +
1138J LEU* 2.4 34.4 + - + +
1140J ARG* 1.3 68.7 - - - +
1142J ALA* 1.3 54.1 + - - +
1143J ASP 3.2 1.1 - - - -
1144J LEU* 2.9 4.6 + - - +
1145J PHE* 2.7 46.8 + - + +
1237J VAL* 3.3 30.7 - - + +
1240J VAL* 3.7 21.5 - - + -
1241J TYR* 4.9 11.7 - - + +
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Residues in contact with ALA1142 (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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795J TYR* 4.8 8.1 - - + +
796J LEU* 3.4 23.6 - - + +
799J ARG* 3.2 29.3 + - - +
1138J LEU 3.3 3.6 + - - -
1139J PRO* 3.9 11.6 + - + +
1141J VAL* 1.3 78.1 - - - +
1143J ASP* 1.3 63.4 + - - +
1145J PHE* 3.3 13.6 + - - +
1146J GLU* 3.4 18.6 + - - +
1309J ILE* 4.5 1.6 - - - +
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Residues in contact with ASP1143 (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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1139J PRO 3.4 18.4 + - - +
1140J ARG* 3.9 18.1 + - - +
1142J ALA* 1.3 79.2 - - - +
1144J LEU* 1.3 57.2 + - - +
1146J GLU* 2.8 26.0 + - - +
1147J ALA* 3.5 4.5 + - - -
1148J ARG* 3.1 49.6 + - - +
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Residues in contact with LEU1144 (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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1140J ARG* 3.0 37.3 + - - +
1141J VAL* 2.9 7.3 + - - +
1143J ASP* 1.3 75.4 - - - +
1145J PHE* 1.3 58.2 + - + +
1146J GLU 3.1 2.8 + - - -
1147J ALA* 4.1 5.6 + - - +
1217J PRO* 5.7 0.7 - - - +
1233J ILE* 4.0 30.7 - - + +
1236J GLU* 3.1 52.0 - - + +
1237J VAL* 3.4 35.0 - - + +
1240J VAL* 4.1 11.0 - - + -
1260J MET* 4.7 1.9 - - - +
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Residues in contact with PHE1145 (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* 5.4 0.7 - - + -
800J LEU* 4.9 9.0 - - + -
923J ILE* 3.8 31.9 - - + -
1141J VAL* 2.7 31.0 + - + +
1142J ALA* 3.5 5.6 - - - +
1143J ASP 3.1 0.2 - - - -
1144J LEU* 1.3 73.6 - - + +
1146J GLU* 1.3 57.6 + - - +
1147J ALA 3.8 0.4 - - - -
1233J ILE* 4.8 7.6 - - + -
1237J VAL* 4.0 19.3 - - + -
1253J ILE* 3.7 31.0 - - + -
1256J ILE* 3.3 36.3 - - + -
1257J VAL 4.7 0.2 - - - -
1260J MET* 3.7 25.8 - - - +
1309J ILE* 3.1 44.3 + - + +
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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