Contacts of the helix formed by residues 1364 - 1377 (chain J) in PDB entry 4XLN
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 HIS1364 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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773J ALA 3.7 7.5 + - - +
774J SER* 4.5 6.4 + - - +
1141J GLU 5.2 0.4 - - - -
1142J SER* 2.3 36.4 + - - +
1143J GLY 3.1 21.8 - - - -
1145J TYR* 2.5 32.1 + + + -
1147J ARG* 3.4 18.4 + - - -
1209J LEU* 4.0 25.4 - - + -
1363J LEU* 1.3 81.4 - - - +
1365J ASP* 1.3 74.5 + - - +
1366J LYS* 3.2 40.5 + - + +
1367J HIS* 3.3 19.1 + - + +
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Residues in contact with ASP1365 (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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1120J VAL* 5.2 5.5 - - - +
1135J ARG* 4.9 4.0 + - - -
1142J SER 3.1 8.3 + - - +
1143J GLY* 3.5 17.1 - - - -
1147J ARG* 4.2 5.2 - - - +
1349J VAL* 4.5 13.7 - - + +
1353J GLN* 2.9 32.8 + - - +
1357J ARG* 3.3 12.4 + - - -
1363J LEU* 4.9 2.5 - - - -
1364J HIS* 1.3 78.3 + - - +
1366J LYS* 1.3 63.2 + - - +
1367J HIS 3.2 0.2 - - - -
1368J ILE* 3.2 9.9 + - - +
1369J GLU* 2.9 41.2 + - + +
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Residues in contact with LYS1366 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1145J TYR 5.0 0.2 + - - -
1146J GLY 4.7 1.0 + - - -
1147J ARG* 3.5 25.5 - - - +
1191J PRO* 4.4 4.4 - - + +
1205J TYR* 3.0 66.9 + - + +
1207J TYR* 2.8 32.7 + - - +
1209J LEU* 3.8 14.6 - - - +
1364J HIS* 3.2 36.6 + - + +
1365J ASP* 1.3 76.4 - - - +
1367J HIS* 1.3 65.2 + - - +
1369J GLU* 3.1 5.2 + - - +
1370J ILE* 2.9 29.9 + - - +
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Residues in contact with HIS1367 (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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772J PRO 3.5 16.7 + - - -
773J ALA* 2.9 28.6 + - - -
1205J TYR* 3.7 22.2 + + - -
1209J LEU* 3.6 8.1 - - + +
1224J VAL* 4.8 2.7 - - + -
1225J ALA* 3.4 41.6 - - + +
1228J SER* 3.9 17.9 - - - -
1229J ILE* 4.1 12.3 - - + -
1363J LEU* 4.6 8.5 - - + -
1364J HIS* 3.3 24.4 - - + +
1366J LYS* 1.3 78.7 - - - +
1368J ILE* 1.3 63.2 + - - +
1370J ILE* 3.3 8.6 + - - +
1371J VAL* 3.3 17.2 + - - +
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Residues in contact with ILE1368 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1229J ILE* 4.1 18.2 - - + -
1263J PHE* 4.7 1.6 - - + -
1349J VAL* 3.8 24.2 - - + +
1352J ILE* 3.6 51.1 - - + -
1353J GLN* 3.6 32.8 - - + +
1356J TYR* 5.2 0.2 - - + -
1363J LEU* 3.7 24.0 - - + -
1365J ASP* 3.2 8.2 + - - +
1367J HIS* 1.3 75.3 - - - +
1369J GLU* 1.3 60.0 + - - +
1371J VAL* 3.2 7.1 + - - +
1372J VAL* 2.9 26.2 + - + +
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Residues in contact with GLU1369 (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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1118J ILE* 4.8 6.6 - - - +
1147J ARG* 3.0 26.6 + - - -
1190J SER* 2.2 33.2 + - - +
1191J PRO* 3.6 7.6 - - + +
1192J LEU* 3.2 27.5 - - + +
1349J VAL* 4.1 18.8 - - + +
1365J ASP* 2.9 26.2 + - + +
1366J LYS* 3.1 9.4 + - - +
1368J ILE* 1.3 74.6 - - - +
1370J ILE* 1.3 66.1 + - - +
1372J VAL* 3.2 8.1 + - - -
1373J ARG* 2.9 20.3 + - - +
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Residues in contact with ILE1370 (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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1102J ALA* 4.5 9.0 - - + -
1105J ILE* 3.7 35.7 - - + -
1191J PRO* 4.0 21.1 - - + +
1200J VAL* 4.7 4.9 - - + -
1205J TYR* 4.1 13.0 - - + -
1221J VAL* 3.6 42.6 - - + +
1222J GLY* 4.7 0.9 - - - -
1225J ALA* 4.1 9.6 - - + -
1366J LYS 2.9 20.7 + - - +
1367J HIS 3.7 4.9 - - - +
1368J ILE 3.3 0.2 - - - -
1369J GLU* 1.3 75.3 - - - +
1371J VAL* 1.3 64.5 + - + +
1373J ARG* 3.2 9.0 + - - +
1374J GLN* 2.9 27.5 + - + +
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Residues in contact with VAL1371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098J LEU* 4.1 11.0 - - + -
1101J VAL* 4.4 8.7 - - + -
1102J ALA* 4.9 11.0 - - + -
1225J ALA* 5.5 2.9 - - + -
1226J ALA* 5.8 1.8 - - - +
1229J ILE* 3.9 19.7 - - + -
1263J PHE* 3.6 24.2 - - + -
1367J HIS 3.3 17.5 - - - +
1368J ILE 3.4 5.6 - - - +
1370J ILE* 1.3 76.0 - - + +
1372J VAL* 1.3 58.3 + - - +
1374J GLN* 2.9 25.9 + - - +
1375J MET* 2.9 18.4 + - + +
1424J VAL* 3.6 25.1 - - + -
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Residues in contact with VAL1372 (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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1192J LEU* 4.0 2.9 - - + -
1345J GLU* 3.7 41.7 - - + +
1348J LEU* 4.0 24.5 - - + -
1349J VAL* 3.6 20.9 - - + -
1352J ILE* 4.8 4.7 - - + -
1368J ILE* 2.9 24.9 + - + +
1369J GLU* 3.5 10.1 - - - +
1371J VAL* 1.3 76.3 - - + +
1373J ARG* 1.3 60.3 + - - +
1375J MET* 3.1 28.0 + - + +
1376J LEU* 3.6 10.4 + - + +
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Residues in contact with ARG1373 (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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1105J ILE* 3.6 14.8 - - - +
1191J PRO* 3.1 23.5 + - - +
1192J LEU* 3.7 27.6 - - + +
1194J CYS* 3.2 23.5 + - - +
1196J THR 3.8 7.5 + - - -
1198J TYR* 5.0 2.4 - - - +
1199J GLY 3.3 31.2 + - - +
1200J VAL* 4.9 4.4 - - - +
1345J GLU* 5.2 0.7 - - - +
1369J GLU 2.9 13.2 + - - +
1370J ILE* 3.5 9.7 + - - +
1372J VAL* 1.3 77.1 - - - +
1374J GLN* 1.3 85.2 + - - +
1375J MET 3.3 0.7 + - - -
1376J LEU* 3.6 14.2 + - + +
1377J LYS* 3.3 27.5 + - + +
1397J LYS* 5.5 5.2 - - - +
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Residues in contact with GLN1374 (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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1101J VAL* 3.6 36.9 + - + +
1102J ALA* 4.4 6.1 - - - -
1104J GLU* 4.1 3.2 + - - +
1105J ILE* 3.2 36.0 - - + +
1370J ILE* 2.9 22.4 + - - +
1371J VAL* 2.9 13.8 + - - +
1373J ARG* 1.3 97.5 + - - +
1375J MET* 1.3 61.5 + - - +
1377J LYS* 3.1 47.0 + - - +
1427J SER* 3.0 19.5 + - - -
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Residues in contact with MET1375 (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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1262J LEU 4.4 7.9 - - - +
1263J PHE* 3.4 57.0 - - + +
1265J ALA* 5.4 1.6 - - - -
1348J LEU* 4.3 21.1 - - + -
1352J ILE* 5.5 2.5 - - + -
1371J VAL* 2.9 23.4 + - + +
1372J VAL* 3.3 13.9 - - + +
1373J ARG 3.1 0.6 - - - -
1374J GLN* 1.3 81.3 - - + +
1376J LEU* 1.3 58.6 + - - +
1377J LYS 3.2 3.0 + - - -
1378J TYR* 4.2 2.4 - - - -
1420J LEU 3.7 1.2 - - - +
1421J LEU* 3.5 11.9 - - + -
1422J MET* 3.3 51.1 + - - +
1423J GLY* 5.1 0.4 - - - -
1424J VAL* 3.9 11.2 - - + +
1427J SER* 4.5 3.8 - - - -
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Residues in contact with LEU1376 (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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1336J LEU* 5.2 5.8 - - + -
1341J PRO* 4.2 23.1 - - + +
1344J VAL* 4.4 14.8 - - + -
1345J GLU* 3.6 40.2 - - + +
1372J VAL* 3.8 13.9 - - + +
1373J ARG* 4.3 9.6 - - + +
1375J MET* 1.3 73.2 - - - +
1377J LYS* 1.3 58.5 + - - +
1378J TYR 2.9 21.2 + - - +
1379J VAL* 4.9 0.2 - - - +
1397J LYS* 3.7 30.3 - - - +
1419J PRO* 5.4 3.6 - - + +
1420J LEU 3.4 16.0 + - - +
1421J LEU* 4.1 13.7 - - + +
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Residues in contact with LYS1377 (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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1101J VAL* 6.0 0.2 - - + -
1104J GLU* 3.0 27.1 + - - -
1105J ILE* 5.4 1.0 - - - +
1198J TYR* 5.5 4.4 - - - +
1373J ARG* 3.3 21.0 + - + +
1374J GLN* 3.1 44.6 + - - +
1375J MET 3.2 0.4 - - - -
1376J LEU* 1.3 77.5 - - - +
1378J TYR* 1.3 80.7 + - + +
1396J GLU* 3.2 30.5 + - - +
1397J LYS* 2.6 46.4 + - + +
1427J SER* 4.5 1.8 - - - +
1431J THR* 5.6 0.8 + - - -
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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