Contacts of the helix formed by residues 1380 - 1392 (chain B) in PDB entry 6V65
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 SER1380 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271B MET* 4.0 7.6 - - - -
1369B TYR* 3.1 16.7 + - - -
1372B VAL* 3.9 21.7 - - - +
1373B SER* 2.9 27.5 + - - -
1376B PHE 3.1 22.7 + - - -
1377B PRO 3.8 7.4 + - - -
1378B GLN 3.2 2.0 - - - -
1379B ASN* 1.3 78.1 - - - +
1381B ILE* 1.3 60.6 + - - +
1382B GLY 3.2 0.9 + - - -
1383B ALA* 3.3 17.4 + - - +
1384B VAL* 3.9 3.5 + - - +
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Residues in contact with ILE1381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1369B TYR* 3.6 17.4 - - + +
1379B ASN* 4.5 2.0 - - - -
1380B SER* 1.3 79.8 + - - +
1382B GLY* 1.3 64.1 + - - +
1383B ALA 3.3 0.2 - - - -
1384B VAL* 3.4 7.3 + - + +
1385B GLY* 3.3 17.2 + - - -
1455B ARG* 3.5 42.4 - - + +
1458B PHE* 3.3 43.6 - - + +
1459B LEU* 3.6 31.2 - - + +
1462B ALA* 3.6 19.1 - - + -
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Residues in contact with GLY1382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271B MET* 5.3 0.9 - - - -
1379B ASN* 3.2 9.9 + - - -
1380B SER 3.1 1.8 - - - -
1381B ILE* 1.3 84.7 - - - +
1383B ALA* 1.3 62.2 + - - +
1385B GLY* 3.4 1.7 + - - -
1386B SER* 3.1 25.1 + - - -
1429B ALA 4.6 7.1 - - - +
1430B ASN* 5.9 0.2 - - - -
1455B ARG* 4.9 6.0 - - - +
1458B PHE* 5.7 3.1 - - - -
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Residues in contact with ALA1383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271B MET* 4.4 19.0 - - + +
1274B LEU* 5.3 13.0 - - + +
1276B ARG* 6.2 0.7 - - - +
1368B LEU* 4.7 4.9 - - + +
1372B VAL* 4.8 14.8 - - + -
1379B ASN 4.4 1.8 + - - -
1380B SER 3.3 10.7 + - - +
1382B GLY* 1.3 76.5 - - - +
1384B VAL* 1.3 63.3 + - + +
1386B SER* 3.1 17.9 + - - -
1387B ALA* 3.3 14.0 + - - +
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Residues in contact with VAL1384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289B PHE* 5.9 0.5 - - - -
1365B CYS* 3.8 34.1 - - + +
1368B LEU* 3.7 33.3 - - + +
1369B TYR* 3.8 27.6 - - + -
1372B VAL* 5.2 1.1 - - + -
1380B SER 3.9 8.5 + - - +
1381B ILE* 3.4 12.5 + - + +
1382B GLY 3.3 1.0 - - - -
1383B ALA* 1.3 78.9 - - - +
1385B GLY* 1.3 59.2 + - - +
1387B ALA* 3.8 1.4 - - - +
1388B MET* 2.8 30.2 + - + +
1458B PHE* 5.1 1.6 - - + +
1461B ILE* 5.1 8.1 - - + -
1462B ALA* 4.4 9.6 - - + -
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Residues in contact with GLY1385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1381B ILE 3.3 8.3 + - - -
1382B GLY 3.4 1.5 + - - -
1384B VAL* 1.3 79.9 - - - +
1386B SER* 1.3 56.7 + - - +
1388B MET* 3.4 4.5 + - - +
1389B PHE* 3.0 27.9 + - - +
1429B ALA* 4.0 0.6 - - - +
1458B PHE* 3.5 48.8 - - - -
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Residues in contact with SER1386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276B ARG* 4.0 24.3 + - - -
1382B GLY 3.1 13.7 + - - -
1383B ALA* 3.1 14.6 + - - -
1385B GLY* 1.3 74.3 - - - +
1387B ALA* 1.3 63.2 + - - +
1389B PHE* 3.1 1.7 + - - -
1390B LEU* 2.6 40.5 + - - +
1426B GLN* 3.5 3.6 - - - +
1429B ALA* 4.4 9.0 + - - -
1430B ASN* 3.4 26.9 - - - -
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Residues in contact with ALA1387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275B PHE* 5.3 6.3 - - + +
1276B ARG* 5.7 0.6 - - - +
1285B MET* 4.0 27.1 - - + -
1289B PHE* 4.2 5.9 - - + -
1368B LEU* 4.9 3.1 - - + -
1383B ALA 3.3 14.0 + - - +
1384B VAL 4.0 2.0 - - - +
1386B SER* 1.3 82.3 + - - +
1388B MET* 1.3 61.4 + - - +
1390B LEU* 4.4 6.7 - - - +
1391B ARG* 3.1 42.5 + - - +
1392B PHE 4.2 0.3 + - - -
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Residues in contact with MET1388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289B PHE* 4.5 21.5 - - + -
1296B TYR* 4.8 1.1 - - + +
1350B ILE* 5.9 1.1 - - + -
1357B PHE* 3.5 39.0 - - + -
1365B CYS* 4.9 2.2 - - - -
1384B VAL* 2.8 22.3 + - + +
1385B GLY* 3.4 8.5 - - - +
1386B SER 3.1 0.2 - - - -
1387B ALA* 1.3 75.7 - - - +
1389B PHE* 1.3 61.3 + - + +
1392B PHE* 3.2 43.3 - - + +
1393B ILE* 3.3 33.3 + - + +
1457B PHE* 4.6 8.5 - - + -
1458B PHE* 4.5 9.9 - - + -
1461B ILE* 4.3 17.3 - - + -
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Residues in contact with PHE1389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347B PHE* 4.9 14.6 - + - -
1350B ILE* 3.8 45.5 - - + -
1351B ILE* 5.5 0.7 - - + -
1385B GLY 3.0 12.9 + - - +
1386B SER 3.8 0.7 - - - +
1388B MET* 1.3 79.5 - - + +
1390B LEU* 1.3 63.9 + - - +
1393B ILE* 3.5 20.4 + - + -
1394B ASN* 2.9 46.4 + - - +
1425B LEU* 4.2 23.1 - - + -
1426B GLN* 3.6 12.3 - - - +
1428B ILE* 6.5 0.2 - - + -
1429B ALA* 3.6 15.3 - - + -
1454B ALA* 5.1 6.3 - - + -
1457B PHE* 5.5 1.8 - + - -
1458B PHE* 3.5 38.8 - + - -
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Residues in contact with LEU1390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276B ARG* 4.7 9.2 - - + +
1386B SER 2.6 23.0 + - - +
1387B ALA* 4.5 2.9 - - - -
1389B PHE* 1.3 75.0 - - - +
1391B ARG* 1.3 67.9 + - + +
1395B PRO* 3.2 10.4 - - - +
1426B GLN* 3.4 25.6 - - + +
34C PRO* 3.6 44.0 - - + +
35C THR 5.2 1.1 - - - +
36C ILE* 5.0 4.9 - - + -
61C GLN* 4.1 22.0 - - + +
63C GLU* 4.9 0.2 - - - +
64C TYR* 2.6 51.6 + - + +
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Residues in contact with ARG1391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275B PHE* 2.3 38.4 + - - +
1276B ARG* 4.4 0.2 - - - +
1277B GLY 2.4 33.3 + - - +
1278B ASN* 4.7 1.6 - - - +
1282B SER* 3.7 17.2 - - - -
1285B MET* 4.7 11.8 - - - -
1286B THR* 3.3 40.7 + - + +
1289B PHE* 4.9 6.8 - - + -
1387B ALA* 3.1 29.8 + - - +
1390B LEU* 1.3 89.2 - - + +
1392B PHE* 1.3 61.0 + - - +
1395B PRO* 3.9 9.4 - - - +
61C GLN* 2.9 20.9 - - + +
63C GLU* 3.6 30.0 + - - +
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Residues in contact with PHE1392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289B PHE* 3.2 49.6 - + + -
1290B LYS* 4.8 2.5 - - - -
1293B GLY* 3.4 33.4 - - - -
1294B ALA* 5.3 0.7 - - - -
1296B TYR* 4.0 13.9 - + - -
1297B LEU* 3.3 37.2 - - + +
1361B LEU* 4.3 9.4 - - + -
1388B MET* 3.2 29.0 + - + +
1390B LEU 3.5 1.2 - - - -
1391B ARG* 1.3 80.6 - - - +
1393B ILE* 1.3 95.0 + - + +
1394B ASN 3.6 0.2 - - - -
1395B PRO* 3.8 6.4 - - - +
1396B ALA* 3.9 5.7 + - - +
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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