Contacts of the helix formed by residues 1364 - 1376 (chain N) in PDB entry 5X22
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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773N ALA 3.4 22.7 + - - +
774N SER* 4.8 5.1 - - - +
1141N GLU 4.3 2.5 - - - -
1142N ALA* 3.2 31.2 + - - -
1145N TYR* 2.8 34.6 + + - -
1147N ARG* 3.9 19.4 - - + +
1209N LEU* 3.8 21.5 - - + -
1353N GLN* 3.7 2.4 + - - -
1363N LEU* 1.3 78.4 - - - +
1365N ASP* 1.3 64.3 + - - +
1366N LYS* 3.0 51.1 + - + +
1367N HIS* 3.1 25.0 + - + +
1368N ILE* 4.3 2.3 + - - +
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Residues in contact with ASP1365 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120N VAL* 6.0 0.3 - - - +
1135N ARG* 4.8 4.2 + - - -
1139N ASP 5.0 0.2 - - - +
1142N ALA* 3.2 28.5 + - - +
1143N GLY* 3.6 17.2 - - - -
1147N ARG* 4.3 2.4 + - - +
1349N VAL* 4.2 13.8 - - + +
1350N GLU* 5.2 1.7 - - - +
1353N GLN* 2.7 33.2 + - - +
1357N ARG* 4.4 9.3 + - - -
1364N HIS* 1.3 70.7 - - - +
1366N LYS* 1.3 63.9 + - - +
1367N HIS 3.3 0.6 + - - -
1368N ILE* 3.3 7.5 + - - +
1369N GLU* 2.9 42.3 + - - +
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Residues in contact with LYS1366 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146N GLY 5.3 1.3 - - - +
1147N ARG* 4.3 16.4 - - + +
1191N PRO* 4.3 6.9 - - + +
1205N TYR* 3.2 61.2 + - + +
1207N TYR* 2.8 29.7 + - - +
1209N LEU* 3.6 21.4 - - - +
1364N HIS* 3.0 41.6 + - + +
1365N ASP* 1.3 77.4 - - - +
1367N HIS* 1.3 61.3 + - + +
1369N GLU* 3.1 12.2 + - - +
1370N ILE* 2.9 32.8 + - - +
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Residues in contact with HIS1367 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772N PRO 3.4 17.6 + - - -
773N ALA* 3.4 20.8 + - - -
1205N TYR* 4.0 20.5 + - - -
1209N LEU* 4.5 2.6 - - + +
1221N VAL 5.2 0.2 + - - -
1224N VAL* 4.3 6.1 - - + -
1225N ALA* 3.3 41.6 + - + +
1228N SER* 3.7 12.3 - - - -
1229N ILE* 4.0 11.4 - - + -
1363N LEU* 4.0 15.3 - - + -
1364N HIS* 3.1 31.7 - - + +
1365N ASP 3.3 0.8 - - - -
1366N LYS* 1.3 73.4 - - + +
1368N ILE* 1.3 61.6 + - + +
1370N ILE* 2.9 21.6 + - - +
1371N VAL* 3.0 16.8 + - - +
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Residues in contact with ILE1368 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1229N ILE* 4.0 20.6 - - + +
1263N PHE* 4.5 2.5 - - + -
1349N VAL* 3.9 23.6 - - + -
1352N ILE* 3.8 46.4 - - + -
1353N GLN* 3.5 42.4 - - + +
1356N TYR* 5.1 0.7 - - + -
1363N LEU* 4.6 11.0 - - + -
1364N HIS 4.4 5.4 - - - +
1365N ASP 3.3 6.9 + - - +
1367N HIS* 1.3 74.5 - - - +
1369N GLU* 1.3 58.5 + - - +
1371N VAL* 3.5 2.9 + - - +
1372N VAL* 2.9 37.2 + - + +
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Residues in contact with GLU1369 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118N ILE* 3.8 7.7 - - - +
1147N ARG* 2.6 33.2 + - - -
1190N SER* 2.3 30.8 + - - +
1191N PRO* 3.6 8.3 - - + +
1192N LEU* 3.3 33.2 + - + +
1349N VAL* 3.8 17.5 - - + +
1365N ASP* 2.9 26.8 + - - +
1366N LYS* 3.3 8.7 - - - +
1367N HIS 3.1 0.2 - - - -
1368N ILE* 1.3 76.0 - - - +
1370N ILE* 1.3 59.6 + - - +
1373N ARG* 2.9 30.7 + - - +
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Residues in contact with ILE1370 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102N THR* 4.3 17.3 - - + -
1105N ILE* 4.1 25.1 - - + -
1191N PRO* 3.5 29.2 - - + -
1200N VAL* 4.1 12.3 - - + -
1205N TYR* 4.5 4.7 - - + -
1221N VAL* 3.5 27.1 - - + -
1222N GLY* 4.5 7.0 - - - -
1225N ALA* 4.4 5.2 - - + -
1366N LYS 2.9 22.2 + - - +
1367N HIS* 2.9 10.5 + - - +
1369N GLU* 1.3 74.6 - - - +
1371N VAL* 1.3 58.5 + - - +
1373N ARG* 3.2 10.7 + - - +
1374N GLN* 2.9 27.6 + - - +
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Residues in contact with VAL1371 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098N LEU* 3.6 20.9 - - + -
1101N VAL* 4.2 1.1 - - + -
1102N THR* 3.7 27.1 - - + -
1225N ALA* 4.9 3.6 - - + -
1226N ALA 5.3 0.9 - - - +
1229N ILE* 3.5 24.2 - - + -
1263N PHE* 3.5 28.9 - - + -
1367N HIS 3.0 14.0 + - - +
1368N ILE 3.9 2.2 - - - +
1370N ILE* 1.3 77.3 - - + +
1372N VAL* 1.3 57.6 + - - +
1374N GLN* 2.9 19.9 + - - +
1375N MET* 2.9 13.0 + - + +
1424N VAL* 3.8 13.5 - - + -
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Residues in contact with VAL1372 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192N LEU* 4.0 6.3 - - + -
1345N GLU* 3.7 40.6 - - + +
1348N LEU* 3.9 26.5 - - + -
1349N VAL* 4.0 11.0 - - + -
1352N ILE* 5.0 0.7 - - + -
1368N ILE* 2.9 32.6 + - + +
1369N GLU* 4.0 3.1 - - - +
1371N VAL* 1.3 72.0 - - - +
1373N ARG* 1.3 57.4 + - - +
1375N MET* 2.9 42.0 + - + +
1376N MET* 2.9 17.2 + - + +
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Residues in contact with ARG1373 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105N ILE* 4.1 14.3 - - - +
1191N PRO* 3.0 28.9 + - - +
1192N LEU* 4.2 18.1 + - + +
1194N CYS* 2.8 30.8 + - - +
1195N GLN 4.5 0.2 - - - -
1196N THR 3.1 13.1 + - - -
1199N GLY 2.6 33.1 + - - +
1200N VAL* 3.3 14.8 - - - +
1345N GLU* 5.3 1.3 - - - +
1369N GLU 2.9 21.0 + - - +
1370N ILE* 3.2 8.3 - - - +
1372N VAL* 1.3 75.7 - - - +
1374N GLN* 1.3 72.2 + - - +
1376N MET* 3.4 15.3 + - - +
1377N LYS* 3.5 10.9 + - - +
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Residues in contact with GLN1374 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101N VAL* 3.8 32.7 + - + +
1102N THR* 4.1 11.7 - - + -
1104N GLU* 4.2 12.1 + - - +
1105N ILE* 3.3 32.3 - - + +
1370N ILE 2.9 15.0 + - - +
1371N VAL* 2.9 13.2 + - - +
1373N ARG* 1.3 91.5 + - - +
1375N MET* 1.3 60.3 + - - +
1377N LYS* 3.3 47.8 - - - +
1427N SER* 3.0 18.7 + - - -
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Residues in contact with MET1375 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101N VAL* 6.0 0.4 - - + -
1262N LEU 4.1 5.8 - - - +
1263N PHE* 3.4 52.9 - - + +
1265N ALA* 5.0 1.6 - - - -
1348N LEU* 4.2 13.9 - - + -
1352N ILE* 4.9 2.5 - - + -
1371N VAL 2.9 9.3 + - - +
1372N VAL* 2.9 47.4 + - + +
1374N GLN* 1.3 78.3 - - + +
1376N MET* 1.3 55.9 + - + +
1377N LYS 3.2 5.2 + - - -
1378N TYR* 4.6 1.0 + - - -
1420N LEU 3.9 3.5 - - - +
1421N LEU* 3.9 12.8 - - + +
1422N MET* 3.5 44.7 + - - +
1423N GLY* 4.4 2.5 - - - -
1424N VAL* 4.1 15.5 - - + +
1427N SER* 4.5 2.5 - - - -
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Residues in contact with MET1376 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336N LEU* 4.6 9.9 - - + -
1341N PRO* 3.8 35.0 - - + -
1344N VAL* 4.5 11.0 - - - -
1345N GLU* 3.5 34.3 - - + +
1372N VAL* 2.9 20.8 + - + +
1373N ARG* 3.4 7.2 + - + +
1374N GLN 3.3 0.6 - - - -
1375N MET* 1.3 75.1 - - - +
1377N LYS* 1.3 62.8 + - - +
1378N TYR 3.0 11.6 + - - +
1397N LYS* 3.9 25.1 + - - +
1419N PRO* 4.8 7.4 - - + -
1420N LEU 4.2 9.7 - - - +
1421N LEU* 3.8 27.1 - - + -
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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
------------------------------------------------------------
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