Contacts of the helix formed by residues 1364 - 1377 (chain A) in PDB entry 2NVX
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 ASN1364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515A GLN 3.2 21.6 + - - +
517A ASN* 3.2 22.0 + - - +
875A ALA* 3.5 9.6 - - + +
878A ILE* 5.0 0.6 - - - +
955A PRO* 4.3 8.0 - - - +
1362A TYR* 3.1 23.3 + - - -
1363A VAL* 1.3 74.0 - - - +
1365A TYR* 1.3 72.6 + - - +
1366A ARG* 2.6 63.2 + - - +
1367A HIS* 3.0 21.8 + - + +
1368A MET* 4.1 1.4 + - - +
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Residues in contact with TYR1365 (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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869A GLY 4.7 3.1 - - - -
870A GLU* 2.8 35.3 + - + -
955A PRO* 6.1 1.1 - - + -
1345A ARG* 2.9 14.7 + - - -
1349A TYR* 3.3 48.2 - + - +
1362A TYR* 4.5 4.0 + - - +
1363A VAL 3.4 4.5 + - - -
1364A ASN* 1.3 78.9 + - - +
1366A ARG* 1.3 69.8 + - - +
1367A HIS 2.9 1.7 + - - -
1368A MET* 3.4 3.5 + - - +
1369A ALA* 2.9 37.7 + - + +
200E ARG* 5.3 0.5 - - - -
201E LYS 5.6 0.2 + - - -
202E SER* 4.0 19.1 + - - -
203E GLU* 3.6 36.8 - - + +
204E THR* 4.4 20.2 - - + -
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Residues in contact with ARG1366 (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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865A GLN* 4.4 3.1 + - - -
868A TYR* 3.3 38.9 - - + +
869A GLY* 3.5 25.3 + - - -
871A ASP* 2.7 29.5 + - - -
873A MET 3.2 11.4 + - - -
875A ALA* 3.6 16.8 - - + -
878A ILE* 3.3 27.5 - - - +
955A PRO* 5.7 1.6 - - - +
1364A ASN* 2.6 58.9 + - - +
1365A TYR* 1.3 84.6 - - - +
1367A HIS* 1.3 62.7 + - + +
1369A ALA* 3.7 3.1 - - - +
1370A LEU* 2.9 29.4 + - - +
204E THR* 3.0 20.6 + - - -
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Residues in contact with HIS1367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A PRO* 2.8 26.8 + - + -
515A GLN 3.7 13.2 + - - -
868A TYR* 3.6 23.1 + - - -
875A ALA* 4.4 6.6 - - + +
1064A VAL* 4.5 1.0 - - + +
1067A LEU* 4.2 17.0 - - + -
1068A ALA* 3.6 36.0 - - - +
1071A SER* 3.7 25.4 + - - -
1072A ILE* 3.8 6.3 - - + +
1363A VAL* 4.1 11.2 - - + -
1364A ASN* 3.0 18.8 + - + +
1365A TYR 2.9 0.4 + - - -
1366A ARG* 1.3 78.7 - - + +
1368A MET* 1.3 69.6 + - - +
1370A LEU* 3.2 3.6 + - - +
1371A LEU* 3.1 19.4 + - - +
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Residues in contact with MET1368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072A ILE* 4.1 17.0 - - + -
1349A TYR* 3.8 29.8 - - + -
1352A VAL* 4.0 29.4 - - + +
1353A TYR* 4.4 14.1 - - + -
1356A ILE* 3.4 33.0 - - + -
1363A VAL* 3.3 46.2 - - + +
1364A ASN 4.1 1.3 + - - +
1365A TYR* 3.4 3.3 + - - +
1367A HIS* 1.3 70.8 - - - +
1369A ALA* 1.3 51.4 + - - +
1370A LEU 2.7 15.1 + - - -
1371A LEU* 2.9 4.8 + - - +
1372A VAL* 2.8 31.8 + - + +
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Residues in contact with ALA1369 (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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865A GLN* 4.1 10.8 + - - +
870A GLU* 4.6 0.7 - - - +
1345A ARG* 4.6 6.7 - - - +
1349A TYR* 4.2 6.4 - - + -
1365A TYR* 2.9 53.7 + - + +
1366A ARG* 3.7 4.9 - - - +
1368A MET* 1.3 75.1 - - - +
1370A LEU* 1.3 57.4 + - - +
1372A VAL* 4.3 4.9 - - - -
1373A ASP* 2.8 36.0 - - - +
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Residues in contact with LEU1370 (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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845A LEU* 5.0 3.8 - - + -
848A ILE* 3.7 23.6 - - + -
856A THR* 3.8 19.1 - - + -
864A ILE* 4.5 9.6 - - + -
865A GLN* 3.5 28.7 - - + +
868A TYR* 5.2 2.7 - - + -
1064A VAL* 4.1 18.4 - - + -
1065A GLY* 4.2 3.1 - - - +
1068A ALA* 3.5 24.0 - - + -
1366A ARG 2.9 18.8 + - - +
1367A HIS 3.5 4.9 - - - +
1368A MET 2.7 4.9 + - - -
1369A ALA* 1.3 71.4 - - - +
1371A LEU* 1.3 67.4 - - - +
1373A ASP* 2.8 15.1 + - - +
1374A VAL* 3.0 20.0 + - + +
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Residues in contact with LEU1371 (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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841A LEU* 3.9 27.8 - - + -
844A ALA* 5.8 0.2 - - + -
845A LEU* 3.9 33.3 - - + +
1072A ILE* 3.8 26.0 - - + -
1105A LEU* 4.1 22.4 - - + -
1352A VAL* 4.6 22.4 - - + -
1367A HIS 3.1 9.4 + - - +
1368A MET 2.9 10.0 + - - +
1370A LEU* 1.3 74.8 - - - +
1372A VAL* 1.3 67.8 + - + +
1374A VAL* 2.9 16.1 + - - +
1375A MET* 3.3 19.6 + - + +
1384A VAL* 4.3 10.8 - - + -
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Residues in contact with VAL1372 (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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1345A ARG* 3.7 35.7 - - + +
1348A LEU* 4.4 13.8 - - + +
1349A TYR* 3.9 30.7 - - + +
1352A VAL* 4.5 12.8 - - + -
1368A MET* 2.8 25.5 + - - +
1369A ALA* 4.2 2.2 - - - +
1371A LEU* 1.3 77.4 - - + +
1373A ASP* 1.3 77.4 + - - +
1374A VAL 3.1 0.3 + - - -
1375A MET* 3.2 19.0 + - - +
1376A THR* 3.2 14.6 + - - +
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Residues in contact with ASP1373 (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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864A ILE* 4.1 17.5 - - + +
865A GLN* 4.5 13.8 + - + +
870A GLU* 4.8 1.0 - - - +
1345A ARG* 2.8 36.4 + - - +
1369A ALA 2.8 22.1 - - - +
1370A LEU* 2.8 9.1 + - - +
1372A VAL* 1.3 81.7 - - - +
1374A VAL* 1.3 57.3 + - - +
1376A THR* 3.6 7.7 - - - -
1377A THR* 3.0 40.1 + - + +
200E ARG* 3.6 14.8 + - - -
208E TYR* 5.4 0.7 - - - -
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Residues in contact with VAL1374 (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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844A ALA* 4.1 20.6 - - + +
845A LEU* 3.7 22.0 - - + -
848A ILE* 4.8 13.5 - - + -
858A ASN* 6.2 1.1 - - - +
864A ILE* 4.2 22.2 - - + -
1370A LEU* 3.2 25.8 - - + +
1371A LEU 2.9 9.3 + - - +
1373A ASP* 1.3 72.9 - - - +
1375A MET* 1.3 66.7 + - + +
1377A THR* 3.0 19.1 + - - +
1378A GLN* 4.4 3.6 + - - +
1382A THR* 4.9 3.5 - - - +
1389A PHE* 6.4 1.8 - - + -
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Residues in contact with MET1375 (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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1104A ILE 3.8 22.2 - - - +
1105A LEU* 4.7 5.4 - - - -
1107A VAL* 3.9 17.0 - - + -
1348A LEU* 3.8 32.1 - - + -
1352A VAL* 6.2 0.9 - - - -
1371A LEU* 3.7 22.0 - - + +
1372A VAL* 3.2 10.8 - - - +
1374A VAL* 1.3 78.9 - - + +
1376A THR* 1.3 57.4 + - - +
1378A GLN 4.3 0.3 + - - -
1380A GLY 3.2 5.2 - - - +
1381A LEU* 4.9 2.5 - - + -
1382A THR* 3.1 59.5 + - - +
1384A VAL* 4.1 27.6 - - + +
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Residues in contact with THR1376 (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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1341A ILE* 3.6 31.2 - - + +
1345A ARG* 4.2 22.7 + - + +
1348A LEU* 4.4 6.8 - - - +
1372A VAL 3.2 13.6 + - - -
1373A ASP* 3.2 12.5 + - - -
1375A MET* 1.3 76.2 - - - +
1377A THR* 1.3 57.6 + - - +
1378A GLN 3.2 5.4 - - - -
1379A GLY* 3.0 21.7 + - - -
1380A GLY 3.5 8.6 - - - +
1381A LEU* 5.2 3.6 - - - +
212E ARG* 3.3 24.9 + - - +
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Residues in contact with THR1377 (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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863A VAL 4.4 4.9 - - - -
864A ILE* 4.0 36.8 - - + +
1373A ASP* 3.0 21.8 + - + +
1374A VAL* 3.0 20.4 + - - +
1375A MET 3.6 0.2 - - - -
1376A THR* 1.3 73.4 - - - +
1378A GLN* 1.3 58.3 + - - +
1379A GLY 3.2 0.4 - - - -
176E PRO* 3.6 24.9 - - + +
177E ARG* 3.1 25.7 + - - +
212E ARG* 3.7 11.7 - - - +
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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
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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