Contacts of the helix formed by residues 1294 - 1315 (chain A) in PDB entry 5N2S
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 VAL1294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197A GLN* 4.3 4.9 - - - +
1200A ILE* 4.7 17.9 - - + +
1289A ASN* 3.1 20.6 - - - +
1290A PHE* 3.0 33.4 + - + +
1292A VAL 3.5 1.2 + - - -
1293A TRP* 1.3 82.2 - - - +
1295A LEU* 1.3 69.1 + - - +
1296A PRO 3.5 0.7 - - - -
1297A PRO* 3.2 6.6 - - - +
1298A LEU* 3.1 40.9 + - + +
1352A TRP* 6.4 0.7 - - + -
1353A LEU* 5.6 0.4 - - + -
1356A HIS* 3.7 25.6 - - + +
2001A 8K8 5.1 4.0 - - + -
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Residues in contact with LEU1295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1290A PHE* 2.9 53.8 + - + +
1291A PHE* 4.5 20.2 - - + +
1294A VAL* 1.3 73.7 - - - +
1296A PRO* 1.3 70.2 - - + +
1298A LEU* 3.1 19.3 + - + +
1299A LEU* 3.0 22.5 + - - +
1353A LEU* 4.6 5.4 - - + -
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Residues in contact with PRO1296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1291A PHE 3.3 25.4 - - - +
1292A VAL* 3.2 24.0 - - + +
1295A LEU* 1.3 89.6 - - + +
1297A PRO* 1.3 67.0 - - + +
1299A LEU* 3.1 8.6 + - + +
1300A LEU* 2.9 35.0 + - + +
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Residues in contact with PRO1297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197A GLN* 5.0 2.5 - - - +
1200A ILE* 3.8 26.0 - - + -
1201A LEU* 5.5 4.3 - - + -
1204A LEU* 4.4 18.5 - - + +
1292A VAL 3.7 7.9 - - - +
1293A TRP* 4.1 15.9 - - + +
1294A VAL 3.2 12.3 - - - +
1296A PRO* 1.3 97.7 - - + +
1298A LEU* 1.3 56.5 + - - +
1300A LEU* 3.4 11.4 + - + +
1301A MET* 2.9 36.7 + - + +
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Residues in contact with LEU1298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1200A ILE* 3.9 23.1 - - + -
1203A LEU* 6.6 0.2 - - + -
1294A VAL* 3.1 30.8 + - + +
1295A LEU* 3.1 22.9 + - + +
1297A PRO* 1.3 75.7 - - - +
1299A LEU* 1.3 64.1 + - - +
1301A MET* 3.2 15.5 + - + +
1302A VAL* 2.9 29.5 + - + +
1345A ALA* 5.5 2.2 - - + +
1348A PHE* 5.4 1.6 - - + -
1349A ALA* 4.2 34.5 - - + +
1353A LEU* 4.8 11.0 - - + -
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Residues in contact with LEU1299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1295A LEU 3.0 12.4 + - - +
1296A PRO* 3.1 9.8 + - + +
1298A LEU* 1.3 74.3 - - - +
1300A LEU* 1.3 76.1 + - + +
1302A VAL* 3.0 11.8 + - + +
1303A LEU* 3.0 46.3 + - + +
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Residues in contact with LEU1300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204A LEU* 4.5 16.4 - - + -
1296A PRO* 2.9 27.6 + - + +
1297A PRO* 3.8 7.9 - - + +
1299A LEU* 1.3 92.0 - - + +
1301A MET* 1.3 57.9 + - - +
1303A LEU* 3.3 12.2 + - + +
1304A ILE* 2.9 39.5 + - + +
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Residues in contact with MET1301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1200A ILE* 4.5 4.7 - - - +
1203A LEU* 3.3 33.7 - - + +
1204A LEU* 3.5 35.2 - - + -
1207A ALA* 4.0 2.7 - - + -
1297A PRO* 2.9 24.7 + - - +
1298A LEU* 3.5 15.9 - - + +
1300A LEU* 1.3 74.8 - - - +
1302A VAL* 1.3 58.4 + - + +
1304A ILE* 3.3 7.5 + - - +
1305A TYR* 2.9 65.0 + - + +
1345A ALA* 3.6 21.8 - - + -
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Residues in contact with VAL1302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1298A LEU* 2.9 22.5 + - + +
1299A LEU* 3.0 11.6 + - + +
1301A MET* 1.3 76.7 - - + +
1303A LEU* 1.3 64.6 + - + +
1305A TYR* 3.4 5.1 + - - +
1306A LEU* 3.0 39.6 + - + +
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Residues in contact with LEU1303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1299A LEU* 3.0 38.7 + - + +
1300A LEU* 3.7 15.9 - - + +
1302A VAL* 1.3 78.1 - - + +
1304A ILE* 1.3 64.0 + - + +
1306A LEU* 3.3 14.5 + - + +
1307A GLU* 3.0 35.8 + - + +
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Residues in contact with ILE1304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204A LEU* 4.0 17.0 - - + -
1207A ALA* 3.4 33.7 - - + +
1208A VAL* 3.9 28.3 - - + -
1211A TYR* 4.0 19.5 - - + -
1300A LEU* 2.9 24.6 + - + +
1301A MET* 3.7 4.5 - - - +
1303A LEU* 1.3 76.2 - - + +
1305A TYR* 1.3 60.1 + - + +
1307A GLU* 3.0 9.6 + - - +
1308A VAL* 2.9 32.9 + - + +
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Residues in contact with TYR1305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203A LEU 4.2 0.5 + - - -
1206A ILE* 4.2 2.9 - - - +
1207A ALA* 3.6 34.9 + - + +
1210A ARG* 4.6 10.8 - - + -
1301A MET* 2.9 50.9 + - + +
1302A VAL* 4.1 3.6 - - - +
1304A ILE* 1.3 79.6 - - + +
1306A LEU* 1.3 61.5 + - - +
1308A VAL* 3.3 11.4 + - + +
1309A PHE* 2.9 38.3 + + + +
1338A ALA* 4.6 7.2 - - + -
1341A ALA* 3.2 35.5 + - + +
1342A ALA* 4.0 31.9 - - + -
1345A ALA* 4.2 5.3 - - + +
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Residues in contact with LEU1306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1302A VAL* 3.0 33.8 + - + +
1303A LEU* 3.5 15.0 - - + +
1304A ILE 3.2 0.2 - - - -
1305A TYR* 1.3 78.1 - - - +
1307A GLU* 1.3 61.1 + - + +
1309A PHE* 3.5 10.1 + - + +
1310A ALA* 2.9 30.0 + - - +
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Residues in contact with GLU1307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211A TYR* 3.7 27.5 + - + +
1303A LEU* 3.0 25.8 + - + +
1304A ILE* 3.4 8.5 - - - +
1306A LEU* 1.3 78.6 - - - +
1308A VAL* 1.3 58.0 + - - +
1310A ALA* 3.2 9.3 + - - +
1311A LEU* 2.9 42.9 + - + +
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Residues in contact with VAL1308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210A ARG* 4.2 9.4 - - + +
1211A TYR* 3.6 38.1 - - + +
1214A VAL* 3.7 24.9 - - + -
1304A ILE* 2.9 25.7 + - + +
1305A TYR* 3.3 10.5 + - + +
1307A GLU* 1.3 76.2 - - - +
1309A PHE* 1.3 63.1 + - + +
1311A LEU* 3.2 2.1 + - - +
1312A ILE* 2.9 46.2 + - + +
1338A ALA* 4.2 16.8 - - + -
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Residues in contact with PHE1309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305A TYR* 2.9 28.6 + + + +
1306A LEU* 4.0 10.8 - - + +
1308A VAL* 1.3 77.1 - - + +
1310A ALA* 1.3 57.0 + - - +
1312A ILE* 4.0 3.4 - - + +
1313A ARG* 2.9 32.3 + - - +
1335A LEU* 4.0 23.7 - - + +
1338A ALA* 3.5 46.9 - - + -
1339A LYS* 3.9 15.9 - - + -
1342A ALA* 4.2 16.2 - - + -
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Residues in contact with ALA1310 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1306A LEU 2.9 18.1 + - - +
1307A GLU* 3.5 13.5 - - - +
1308A VAL 3.2 0.2 - - - -
1309A PHE* 1.3 78.4 - - - +
1311A LEU* 1.3 61.8 + - + +
1313A ARG* 3.3 5.9 + - - +
1314A LYS* 2.9 30.9 + - - +
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Residues in contact with LEU1311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211A TYR* 4.2 14.8 - - + +
1214A VAL* 4.3 14.8 - - + +
1215A LYS* 3.7 47.1 - - + +
1307A GLU* 2.9 28.6 + - + +
1308A VAL* 3.8 3.6 - - - +
1310A ALA* 1.3 79.1 - - + +
1312A ILE* 1.3 58.6 + - - +
1314A LYS* 3.3 5.5 + - + +
1315A GLN* 2.9 38.5 + - + +
1331A TYR* 5.5 0.7 - - - -
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Residues in contact with ILE1312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1214A VAL* 3.7 32.3 - - + -
1308A VAL* 2.9 30.0 + - + +
1309A PHE* 4.1 5.2 - - + +
1311A LEU* 1.3 75.7 - - - +
1313A ARG* 1.3 63.5 + - - +
1315A GLN* 3.6 5.9 + - - +
1316A LEU* 3.7 22.8 - - + +
1331A TYR* 3.7 36.5 - - + +
1334A GLU* 3.9 21.1 - - + +
1335A LEU* 3.8 32.3 - - + +
1338A ALA* 4.4 3.1 - - + -
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Residues in contact with ARG1313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309A PHE 2.9 19.9 + - - +
1310A ALA* 3.7 6.3 - - - +
1312A ILE* 1.3 78.3 - - - +
1314A LYS* 1.3 62.4 + - - +
1316A LEU* 3.3 19.7 + - - +
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Residues in contact with LYS1314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1310A ALA 2.9 16.5 + - - +
1311A LEU* 4.0 5.8 - - + +
1313A ARG* 1.3 71.9 - - - +
1315A GLN* 1.3 59.1 + - + +
1316A LEU* 2.9 15.8 + - - +
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Residues in contact with GLN1315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1214A VAL 5.1 3.9 + - - +
1311A LEU* 2.9 23.3 + - + +
1312A ILE 4.0 1.3 - - - +
1313A ARG 3.3 0.8 - - - -
1314A LYS* 1.3 74.8 - - + +
1316A LEU* 1.3 69.3 + - - +
1328A GLN* 5.0 2.3 + - - -
1331A TYR* 2.9 51.7 + - + -
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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
------------------------------------------------------------
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