Contacts of the helix formed by residues 1254 - 1264 (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 GLN1254 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1253J THR* 1.3 75.6 - - + +
1255J GLY* 1.3 64.6 + - - +
1257J PRO* 3.6 17.5 - - - +
1258J ARG* 3.4 43.9 + - + +
1261J GLU* 4.4 4.2 - - - +
1269J LYS* 3.1 32.6 + - - +
1355J VAL* 4.8 4.5 - - + -
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Residues in contact with GLY1255 (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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1236J LEU* 4.2 4.5 - - - -
1237J THR 5.0 1.8 - - - -
1253J THR* 3.1 10.6 - - - +
1254J GLN* 1.3 79.8 - - - +
1256J LEU* 1.3 62.6 - - - -
1257J PRO* 4.3 1.6 - - - -
1258J ARG* 3.1 18.5 + - - +
1259J VAL 3.4 2.9 + - - -
1355J VAL* 3.5 22.5 - - - +
1359J GLN* 4.1 17.5 - - - -
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Residues in contact with LEU1256 (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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1087J ARG* 3.8 26.7 - - + +
1090J ASP* 4.0 19.1 - - + -
1091J SER* 4.1 6.7 - - - +
1094J LEU* 4.0 28.3 - - + -
1233J GLY* 3.8 23.1 - - - +
1236J LEU* 3.5 39.5 + - + +
1255J GLY* 1.3 68.9 - - - -
1257J PRO* 1.4 74.8 - - + +
1259J VAL* 2.9 19.5 + - + +
1260J ILE* 2.9 21.5 + - + +
1356J TYR* 5.2 1.6 - - - +
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Residues in contact with PRO1257 (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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1087J ARG* 5.4 10.3 - - + -
1236J LEU 5.6 0.2 - - - +
1254J GLN* 3.6 10.8 - - - +
1255J GLY* 3.5 4.3 - - - -
1256J LEU* 1.4 95.2 - - + +
1258J ARG* 1.3 54.9 + - - +
1260J ILE* 3.5 11.2 + - + +
1261J GLU* 2.9 30.6 + - - +
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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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1254J GLN* 3.4 40.7 + - + +
1255J GLY 3.1 11.8 + - - +
1256J LEU 3.1 0.6 - - - -
1257J PRO* 1.3 75.6 - - - +
1259J VAL* 1.3 60.9 + - - +
1261J GLU* 2.9 26.1 + - - +
1262J LEU* 2.9 59.6 + - + +
1268J PRO* 5.1 2.2 - - - +
1269J LYS* 5.3 2.6 - - - +
1329J ALA* 3.4 26.9 - - - +
1347J TYR* 3.0 26.5 + - - -
1351J GLU* 3.2 30.5 + - - +
1355J VAL* 3.6 22.0 - - + -
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Residues in contact with VAL1259 (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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1094J LEU* 3.7 14.1 - - + -
1236J LEU* 3.8 14.1 - - + -
1255J GLY 3.6 14.4 - - - +
1256J LEU* 2.9 11.1 + - + +
1258J ARG* 1.3 75.5 - - - +
1260J ILE* 1.3 58.4 + - - +
1262J LEU* 3.3 9.7 + - - +
1263J PHE* 2.9 62.3 + - + -
1352J ILE* 4.3 4.3 - - + -
1355J VAL* 3.7 23.6 - - + -
1356J TYR* 3.8 22.4 - - + +
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Residues in contact with ILE1260 (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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1090J ASP* 4.4 21.8 - - + +
1093J TYR* 4.0 38.4 - - + -
1094J LEU* 4.1 15.9 - - + -
1256J LEU* 2.9 40.3 + - + +
1257J PRO* 3.8 10.5 - - + +
1259J VAL* 1.3 72.2 - - - +
1261J GLU* 1.3 60.8 + - - +
1262J LEU 3.0 2.0 - - - -
1263J PHE* 4.4 5.4 - - - +
1264J GLU* 2.9 35.1 + - + +
1266J ARG* 4.1 19.7 - - - +
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Residues in contact with GLU1261 (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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1254J GLN* 4.4 6.8 - - - +
1257J PRO 2.9 16.3 + - - +
1258J ARG* 2.9 36.9 + - - +
1260J ILE* 1.3 75.8 - - - +
1262J LEU* 1.3 57.7 + - + +
1265J ALA* 3.5 1.2 + - - -
1266J ARG* 3.0 57.3 + - + +
1267J ARG 4.9 1.8 - - - +
1268J PRO* 3.3 29.9 - - + +
1269J LYS* 3.8 26.0 + - - +
1332J PRO* 5.5 1.0 - - - +
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Residues in contact with LEU1262 (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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1258J ARG* 2.9 59.3 + - + +
1259J VAL* 3.5 7.4 - - - +
1260J ILE 3.0 0.2 - - - -
1261J GLU* 1.3 78.1 - - + +
1263J PHE* 1.3 58.5 + - - +
1264J GLU 3.0 1.6 - - - -
1265J ALA* 2.7 27.0 + - - +
1332J PRO* 5.7 6.3 - - + -
1347J TYR* 4.8 9.4 - - + -
1348J LEU* 4.4 20.3 - - + +
1351J GLU* 3.6 15.7 - - + -
1352J ILE* 3.5 46.9 - - + +
1355J VAL* 5.3 0.2 - - + -
1375J MET* 4.4 6.8 - - - +
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Residues in contact with PHE1263 (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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1094J LEU* 3.9 21.5 - - + -
1098J LEU* 3.5 21.1 - - + -
1229J ILE* 4.1 28.5 - - + -
1259J VAL* 2.9 52.7 + - + +
1260J ILE* 4.3 1.6 - - + +
1262J LEU* 1.3 72.9 - - - +
1264J GLU* 1.3 56.2 + - - +
1352J ILE* 3.5 36.3 - - + +
1368J ILE* 4.7 4.7 - - + -
1371J VAL* 3.6 27.4 - - + -
1372J VAL* 5.6 0.4 - - + -
1375J MET* 3.4 27.9 - - + +
1423J GLY* 3.3 3.5 - - - -
1424J VAL* 2.9 29.8 + - + +
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Residues in contact with GLU1264 (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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1093J TYR* 4.3 5.0 + - - -
1094J LEU* 5.9 0.9 - - - +
1097J LYS* 4.2 7.8 + - - +
1260J ILE* 2.9 21.2 + - + +
1263J PHE* 1.3 75.2 - - - +
1265J ALA* 1.3 70.7 + - - +
1266J ARG* 3.1 45.8 + - + +
1423J GLY* 3.3 14.2 + - - -
1424J VAL* 3.1 20.1 + - - +
1425J THR* 2.7 49.1 + - - -
1426J LYS* 4.3 1.2 + - - +
43R G 5.4 3.1 + - - +
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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