Contacts of the helix formed by residues 1340 - 1359 (chain A) in PDB entry 4V1M
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 GLY1340 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335A ILE 3.8 0.2 - - - +
1336A MET* 3.2 26.0 + - - +
1339A LEU* 1.3 80.2 - - - +
1341A ILE* 1.3 60.7 + - - -
1342A GLU 3.3 2.9 - - - -
1344A GLY 3.1 19.8 + - - -
182E ASP* 3.5 20.2 - - - -
183E PRO* 3.5 11.3 - - - +
184E VAL* 4.5 2.5 - - - -
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Residues in contact with ILE1341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1336A MET* 4.2 17.2 + - + +
1340A GLY* 1.3 70.1 - - - -
1342A GLU* 1.3 61.4 + - + +
1344A GLY* 3.2 2.0 + - - +
1345A ARG* 3.0 25.9 + - - +
1376A THR* 3.4 41.9 - - + +
1379A GLY 3.3 24.5 - - - +
1380A GLY* 3.8 14.4 - - - +
1381A LEU* 5.8 1.1 - - + -
177E ARG 4.7 2.7 - - - +
178E ILE* 4.4 8.3 - - + -
182E ASP* 2.8 21.1 + - - +
212E ARG* 3.5 39.0 - - - +
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Residues in contact with GLU1342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339A LEU 5.7 0.4 - - - +
1340A GLY* 3.3 1.5 - - - -
1341A ILE* 1.3 79.7 - - - +
1343A ALA* 1.3 59.7 - - - +
1345A ARG* 3.3 10.2 + - - +
1346A ALA* 3.3 19.2 + - - +
149E LEU 4.2 2.2 - - - +
150E VAL* 5.5 1.6 - - + -
151E PRO* 3.6 20.1 - - + +
153E HIS* 3.6 31.8 + - + +
184E VAL* 6.1 0.4 - - + -
198E ILE* 3.8 24.8 - - + +
200E ARG* 3.0 32.7 + - - -
210E SER* 5.1 2.4 + - - -
212E ARG* 2.7 37.7 + - - +
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Residues in contact with ALA1343 (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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1335A ILE* 3.4 13.3 - - + +
1339A LEU* 3.6 38.9 + - + +
1340A GLY 3.6 1.6 + - - +
1341A ILE 3.4 0.2 - - - -
1342A GLU* 1.3 75.6 - - - +
1344A GLY* 1.3 56.0 + - - +
1346A ALA* 3.2 2.8 + - - +
1347A ALA 2.8 31.2 + - - -
149E LEU* 3.4 35.5 + - + +
150E VAL* 4.2 0.9 - - + -
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Residues in contact with GLY1344 (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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1332A PHE* 4.3 6.6 - - - +
1335A ILE* 3.8 9.8 - - - +
1336A MET* 4.1 20.6 - - - -
1340A GLY 3.1 15.5 + - - -
1341A ILE* 3.2 6.6 + - - -
1343A ALA* 1.3 76.7 - - - +
1345A ARG* 1.4 49.5 + - - +
1347A ALA* 3.6 1.9 + - - +
1348A LEU* 2.9 36.3 + - - +
1376A THR* 4.9 2.2 - - - -
1381A LEU* 5.4 3.8 - - - -
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Residues in contact with ARG1345 (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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870A GLU* 3.6 10.9 + - - -
1341A ILE 3.0 11.0 + - - +
1342A GLU* 3.3 14.5 + - - +
1344A GLY* 1.4 72.0 - - - +
1346A ALA* 1.3 65.8 + - - +
1348A LEU* 3.3 2.9 + - - -
1349A TYR* 2.9 37.6 + - - +
1365A TYR* 3.3 26.1 + - - -
1369A ALA* 3.8 11.7 + - - +
1372A VAL* 3.3 33.4 - - + +
1373A ASP* 2.8 46.4 + - - +
1376A THR* 3.7 32.4 + - + +
200E ARG* 3.4 35.9 - - - +
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Residues in contact with ALA1346 (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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1342A GLU 3.3 8.2 + - - +
1343A ALA* 3.2 10.9 + - - +
1345A ARG* 1.3 86.6 - - - +
1347A ALA* 1.3 56.5 + - - +
1349A TYR* 3.9 6.5 - - - +
1350A LYS* 3.0 28.4 + - - +
149E LEU* 3.6 31.1 - - + +
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Residues in contact with ALA1347 (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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1328A TYR* 3.6 19.8 + - + +
1332A PHE* 3.8 18.2 - - + -
1335A ILE* 3.7 26.5 - - + -
1343A ALA 2.8 19.1 + - - +
1344A GLY 3.8 0.9 - - - +
1346A ALA* 1.3 68.5 - - - +
1348A LEU* 1.4 60.9 + - - +
1350A LYS* 3.1 8.9 + - - +
1351A GLU* 2.9 30.3 + - - +
149E LEU* 4.4 3.5 - - + +
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Residues in contact with LEU1348 (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 28.5 - - + -
1332A PHE* 3.8 32.2 - - + +
1344A GLY 2.9 19.5 + - - +
1345A ARG 3.6 3.1 - - - +
1347A ALA* 1.4 75.6 - - - +
1349A TYR* 1.4 58.9 + - - +
1351A GLU* 3.5 2.9 + - - +
1352A VAL* 3.0 29.5 + - + +
1372A VAL* 3.7 36.3 - - + +
1375A MET* 4.0 28.0 - - + -
1376A THR* 4.4 6.3 - - - +
1381A LEU* 3.9 17.0 - - + -
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Residues in contact with TYR1349 (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* 2.9 26.2 + - - +
1346A ALA* 3.9 5.2 - - - +
1348A LEU* 1.4 70.5 - - - +
1350A LYS* 1.4 63.9 + - + +
1352A VAL* 3.0 2.9 + - - +
1353A TYR* 2.7 56.2 + + + -
1365A TYR* 3.3 42.6 - + - -
1368A MET* 3.5 51.8 - - + +
1369A ALA* 3.9 12.6 - - - -
1372A VAL* 3.5 18.3 - - + +
203E GLU* 3.9 16.9 + - - -
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Residues in contact with LYS1350 (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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1119A TYR* 5.7 2.8 + - - -
1328A TYR* 3.8 44.2 - - + +
1346A ALA 3.0 16.1 + - - +
1347A ALA* 3.3 9.6 - - - +
1349A TYR* 1.4 80.8 - - - +
1351A GLU* 1.3 53.4 - - - +
1353A TYR* 3.4 6.6 + - + +
1354A ASN* 2.7 49.8 + - - +
148E GLU* 5.9 0.8 + - - -
149E LEU* 5.6 8.2 - - + +
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Residues in contact with GLU1351 (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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1100A ARG* 2.7 42.3 + - - +
1104A ILE* 3.6 16.9 - - + +
1328A TYR* 2.7 36.1 + - - +
1330A ASN* 3.5 21.7 - - - +
1332A PHE* 4.4 10.8 - - + -
1347A ALA 2.9 13.1 + - - +
1348A LEU 3.6 5.2 - - - +
1350A LYS* 1.3 73.6 - - - +
1352A VAL* 1.4 66.6 - - - +
1354A ASN* 3.4 17.6 + - - +
1355A VAL* 3.3 15.6 + - - +
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Residues in contact with VAL1352 (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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1072A ILE* 5.0 6.3 - - + -
1101A LEU* 5.3 7.9 - - + -
1104A ILE* 3.9 27.6 - - + -
1348A LEU* 3.0 20.2 + - + +
1349A TYR* 3.0 8.1 + - - +
1351A GLU* 1.4 70.8 - - - +
1353A TYR* 1.3 67.7 + - - +
1355A VAL* 3.1 15.0 + - - +
1356A ILE* 3.2 31.1 + - + +
1368A MET* 4.1 19.3 - - + -
1371A LEU* 4.6 22.4 - - + -
1372A VAL* 4.1 12.8 - - + -
1375A MET* 6.1 0.2 - - - -
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Residues in contact with TYR1353 (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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1349A TYR* 2.7 46.5 + + + +
1350A LYS* 3.5 6.7 - - + +
1352A VAL* 1.3 72.6 - - - +
1354A ASN* 1.3 76.3 + - - +
1356A ILE* 3.2 6.2 + - + +
1357A ALA* 3.0 44.5 + - + +
1361A SER 5.8 1.6 - - - -
1362A TYR* 5.5 12.3 - + - -
1368A MET* 4.0 27.1 - - + -
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Residues in contact with ASN1354 (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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1350A LYS* 2.7 48.5 + - - +
1351A GLU* 3.7 16.3 + - - +
1352A VAL 3.3 0.2 - - - -
1353A TYR* 1.3 86.1 - - - +
1355A VAL* 1.4 54.9 + - - +
1356A ILE 3.2 0.2 + - - -
1357A ALA* 4.6 3.0 - - - +
1358A SER* 2.7 39.2 + - - -
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Residues in contact with VAL1355 (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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1079A MET* 3.8 20.5 - - + +
1096A SER* 4.3 2.0 - - - -
1097A GLY* 3.3 39.3 - - - +
1100A ARG* 3.7 22.2 - - + -
1101A LEU* 3.9 33.0 - - + +
1104A ILE* 4.5 2.7 - - + -
1351A GLU 3.3 8.0 + - - +
1352A VAL 3.1 13.1 + - - +
1354A ASN* 1.4 76.0 - - - +
1356A ILE* 1.3 71.5 + - + +
1358A SER* 3.0 18.0 + - - -
1359A ASP 3.9 0.7 + - - -
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Residues in contact with ILE1356 (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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1072A ILE* 4.4 18.4 - - + +
1075A PRO* 5.2 7.6 - - + -
1076A ALA* 6.2 0.9 - - - +
1079A MET* 5.2 5.4 - - + -
1101A LEU* 5.8 1.3 - - + -
1352A VAL* 3.2 34.2 + - + +
1353A TYR* 3.2 8.5 + - + +
1355A VAL* 1.3 85.9 - - + +
1357A ALA* 1.3 63.8 + - + +
1359A ASP* 3.2 14.1 + - - +
1361A SER* 3.3 44.0 + - - +
1362A TYR* 4.5 0.2 - - - -
1363A VAL* 3.6 34.1 - - + +
1368A MET* 3.8 21.5 - - - -
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Residues in contact with ALA1357 (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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1353A TYR* 3.0 46.7 + - + +
1354A ASN* 4.1 4.5 - - - +
1356A ILE* 1.3 73.9 - - - +
1358A SER* 1.4 58.9 + - - +
1360A GLY* 3.0 19.2 + - - -
1361A SER 3.6 13.7 - - - +
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Residues in contact with SER1358 (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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1096A SER* 4.6 10.0 - - - -
1097A GLY* 4.5 11.4 + - - -
1354A ASN* 2.7 20.7 + - - -
1355A VAL* 3.0 21.5 + - - -
1357A ALA* 1.4 67.4 - - - +
1359A ASP* 1.3 58.0 + - - +
1360A GLY* 3.1 8.5 + - - -
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Residues in contact with ASP1359 (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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1075A PRO 4.8 1.0 - - - +
1078A GLN* 3.2 18.2 - - - +
1079A MET* 3.8 42.0 - - - +
1080A THR* 3.8 12.1 + - - +
1355A VAL 4.2 1.1 - - - +
1356A ILE 3.2 11.8 + - - +
1358A SER* 1.3 79.1 + - - +
1360A GLY* 1.3 61.6 + - - +
1361A SER* 3.3 13.4 + - - +
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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
------------------------------------------------------------
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