Contacts of the helix formed by residues 1267 - 1286 (chain B) in PDB entry 1VDV
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 GLY1267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199B PHE* 3.4 35.4 - - - -
1202B GLY 4.3 0.2 - - - -
1203B LEU* 4.1 11.0 - - - -
1206B PHE* 3.9 9.8 - - - +
1264B LEU 3.0 8.8 + - - -
1265B PHE 2.8 3.0 + - - -
1266B LEU* 1.3 77.6 - - - +
1268B ALA* 1.3 60.6 + - - +
1269B SER 3.1 0.4 - - - -
1270B VAL* 3.2 23.0 + - - +
1271B PHE 3.9 1.4 + - - -
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Residues in contact with ALA1268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921B PHE* 4.8 0.4 - - + -
1001B ILE* 4.9 2.2 - - + -
1206B PHE* 3.6 21.9 - - + -
1265B PHE* 2.8 44.9 + - + +
1266B LEU* 5.3 0.2 - - - -
1267B GLY* 1.3 73.7 - - - +
1269B SER* 1.3 64.7 + - - +
1270B VAL 3.0 2.5 - - - -
1271B PHE* 2.8 17.1 + - + +
1272B PHE* 3.0 31.0 + - + -
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Residues in contact with SER1269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999B CYS* 3.8 11.9 - - - +
1001B ILE* 4.1 19.7 - - - +
1158B ALA* 3.6 27.3 - - - +
1160B SER* 2.7 31.3 + - - -
1199B PHE* 3.8 4.9 - - - -
1266B LEU 2.9 21.1 + - - -
1267B GLY 3.1 0.2 - - - -
1268B ALA* 1.3 78.4 - - - +
1270B VAL* 1.3 57.0 + - - +
1272B PHE 3.6 0.3 + - - -
1273B ALA* 3.0 27.9 + - - +
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Residues in contact with VAL1270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160B SER* 3.7 23.6 - - - +
1162B VAL* 3.9 8.3 - - + -
1171B HIS* 4.3 0.4 - - - +
1173B ASN* 3.3 29.2 - - + +
1176B THR* 4.4 2.7 - - - +
1199B PHE* 3.9 17.0 - - + -
1203B LEU* 3.7 24.5 - - + -
1207B THR* 4.1 2.9 - - + -
1236B PRO* 6.3 0.4 - - + -
1267B GLY 3.2 12.8 + - - +
1268B ALA 3.0 0.8 - - - -
1269B SER* 1.3 75.1 - - - +
1271B PHE* 1.3 65.6 + - - +
1273B ALA* 3.2 4.0 + - - +
1274B ILE* 2.9 40.8 + - + +
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Residues in contact with PHE1271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921B PHE* 3.6 36.1 - + + -
925B ASN* 5.6 1.6 - - - -
1206B PHE* 3.3 37.0 - - + -
1207B THR* 4.4 6.4 - - - +
1267B GLY 3.9 1.0 + - - -
1268B ALA* 2.8 12.4 + - - +
1270B VAL* 1.3 79.1 - - - +
1272B PHE* 1.3 80.7 + + + +
1274B ILE* 3.2 9.6 + - - +
1275B LYS* 3.0 27.0 + - + +
1296B LEU* 3.4 44.5 - - + +
1297B ASP 3.7 10.8 - - - -
1298B SER* 4.0 2.2 - - - -
1300B ALA* 3.5 24.7 - - + -
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Residues in contact with PHE1272 (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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921B PHE* 3.9 27.6 - + - -
924B GLU* 3.5 42.2 - - + -
925B ASN* 3.7 20.2 - - - -
928B SER* 4.2 18.6 - - - -
942B ARG* 4.8 2.2 - - - +
999B CYS* 3.4 25.8 - - - +
1001B ILE* 4.5 9.6 - - + -
1265B PHE* 5.0 0.2 - + - -
1268B ALA* 3.0 34.1 + - + +
1271B PHE* 1.3 92.0 - + - +
1273B ALA* 1.3 60.1 + - - +
1274B ILE 3.1 0.4 - - - -
1275B LYS* 3.6 13.1 - - + +
1276B ASP* 2.9 27.9 + - - +
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Residues in contact with ALA1273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B GLY* 3.2 22.8 - - - +
998B LEU 4.1 4.9 - - - +
999B CYS* 3.7 9.4 - - - +
1160B SER 3.5 22.7 - - - +
1162B VAL* 3.8 15.5 - - + -
1269B SER 3.0 18.9 + - - +
1270B VAL 3.5 6.1 - - - +
1272B PHE* 1.3 77.1 - - - +
1274B ILE* 1.3 58.9 + - - +
1276B ASP* 3.2 1.7 + - - +
1277B ALA* 3.0 23.2 + - - +
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Residues in contact with ILE1274 (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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1162B VAL* 3.8 21.5 - - + -
1164B ILE* 4.3 5.2 - - + -
1171B HIS* 3.7 33.4 - - + +
1207B THR* 3.8 24.0 - - + -
1270B VAL* 2.9 19.5 + - + +
1271B PHE* 3.3 9.0 - - - +
1273B ALA* 1.3 75.1 - - - +
1275B LYS* 1.3 61.8 + - - +
1277B ALA* 3.1 4.6 + - - +
1278B ILE* 2.9 37.7 + - + +
1296B LEU* 5.0 0.7 - - + -
1300B ALA* 4.4 9.0 - - + +
1305B ILE* 3.7 32.1 - - + -
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Residues in contact with LYS1275 (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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925B ASN* 3.4 23.8 + - - -
928B SER* 3.9 15.4 + - - +
929B GLU* 4.5 11.3 + - - +
1271B PHE* 3.0 16.3 + - + +
1272B PHE* 3.7 25.8 - - + +
1273B ALA 3.3 0.2 - - - -
1274B ILE* 1.3 75.6 - - - +
1276B ASP* 1.3 57.0 + - - +
1278B ILE* 3.3 6.5 + - - +
1279B ARG* 3.0 35.6 + - - +
1294B PHE* 3.7 43.9 + - + -
1295B ARG* 5.4 0.4 - - - +
1296B LEU* 3.9 32.1 + - + +
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Residues in contact with ASP1276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984B VAL* 5.0 3.8 - - - +
996B ARG 4.5 2.3 - - - +
997B GLY* 3.6 5.4 - - - -
998B LEU* 3.2 32.5 + - - +
999B CYS* 5.5 0.2 - - + -
1272B PHE 2.9 13.6 + - - +
1273B ALA 3.2 11.0 - - - +
1275B LYS* 1.3 78.4 - - - +
1277B ALA* 1.3 61.2 + - - +
1279B ARG* 3.3 15.0 + - - +
1280B ALA* 3.3 18.5 + - - +
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Residues in contact with ALA1277 (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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995B LYS* 3.6 10.2 - - - +
996B ARG 3.7 30.1 - - - -
997B GLY* 3.7 1.5 - - - +
1162B VAL* 4.5 1.3 - - + -
1164B ILE* 3.7 29.8 - - + -
1273B ALA 3.0 11.0 + - - +
1274B ILE* 3.4 8.7 - - - +
1276B ASP* 1.3 75.6 - - - +
1278B ILE* 1.3 64.2 + - - +
1280B ALA* 3.1 7.4 + - - +
1281B ALA* 3.0 17.5 + - - +
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Residues in contact with ILE1278 (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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1164B ILE* 4.0 17.3 - - + -
1274B ILE* 2.9 32.2 + - + +
1275B LYS 3.3 7.4 + - - +
1277B ALA* 1.3 76.3 - - - +
1279B ARG* 1.3 57.0 + - - +
1281B ALA* 3.1 4.3 + - - +
1282B ARG* 2.8 35.3 + - + +
1294B PHE* 3.6 17.9 - - + -
1296B LEU* 4.1 21.3 - - + -
1305B ILE* 4.0 29.4 - - + +
1308B ALA* 3.6 30.3 - - + +
1309B CYS* 4.6 3.1 - - - -
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Residues in contact with ARG1279 (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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932B VAL* 3.9 28.4 - - - +
1275B LYS* 3.0 20.6 + - - +
1276B ASP* 3.4 18.4 - - - +
1277B ALA 3.2 0.2 - - - -
1278B ILE* 1.3 78.4 - - - +
1280B ALA* 1.3 60.1 + - - +
1282B ARG* 3.3 5.2 + - - +
1283B ALA* 3.0 24.5 + - + +
1290B THR* 4.3 15.0 + - - +
1292B GLU* 2.7 45.2 + - - +
1293B LEU* 4.2 5.7 - - - +
1294B PHE* 3.5 35.3 - - + +
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Residues in contact with ALA1280 (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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988B ASN* 3.6 34.3 - - + +
995B LYS* 4.0 10.2 + - + -
1276B ASP 3.3 8.6 + - - +
1277B ALA* 3.1 11.0 + - - +
1279B ARG* 1.3 79.9 - - - +
1281B ALA* 1.3 62.0 + - - +
1283B ALA* 3.3 8.5 + - - +
1284B GLN* 3.1 20.6 + - - +
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Residues in contact with ALA1281 (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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992B CYS 6.0 0.2 - - - -
995B LYS* 3.8 7.4 - - + +
1164B ILE* 4.6 0.4 - - + -
1166B CYS* 3.8 19.7 - - + -
1277B ALA 3.0 11.6 + - - +
1278B ILE* 3.1 8.9 + - - +
1280B ALA* 1.3 75.2 - - - +
1282B ARG* 1.3 61.6 + - - +
1284B GLN* 3.0 24.8 + - - +
1285B HIS* 3.0 13.3 + - - +
1286B THR* 4.5 0.3 + - - -
1309B CYS* 3.8 31.1 - - + -
1310B VAL 5.1 1.3 - - - +
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Residues in contact with ARG1282 (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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1278B ILE* 2.8 21.2 + - + +
1279B ARG* 3.8 5.4 - - - +
1281B ALA* 1.3 71.8 - - - +
1283B ALA* 1.3 58.8 + - - +
1284B GLN 2.9 5.2 - - - -
1286B THR* 2.5 54.3 + - - +
1287B ASN* 3.3 12.5 - - + +
1288B ASN 5.2 0.7 - - - -
1292B GLU* 2.7 43.1 + - - +
1294B PHE* 3.5 44.2 - - - +
1308B ALA* 2.7 50.6 + - - +
1309B CYS* 4.9 1.3 - - - -
1310B VAL* 3.5 18.6 - - - +
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Residues in contact with ALA1283 (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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1279B ARG* 3.0 18.4 + - + +
1280B ALA* 3.6 9.0 - - - +
1281B ALA 3.3 0.2 - - - -
1282B ARG* 1.3 76.7 - - - +
1284B GLN* 1.3 58.2 + - - +
1286B THR 4.6 0.7 - - - -
1288B ASN* 2.8 31.9 - - - +
1290B THR* 6.3 2.9 - - - +
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Residues in contact with GLN1284 (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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988B ASN 4.2 2.2 + - - -
989B LYS 5.6 1.8 + - - -
991B ASN 3.6 1.4 + - - -
992B CYS* 3.3 32.4 - - - +
995B LYS* 2.8 30.4 - - - +
1280B ALA 3.1 13.1 + - - +
1281B ALA* 3.0 15.3 - - - +
1282B ARG 2.9 1.2 - - - -
1283B ALA* 1.3 81.4 - - - +
1285B HIS* 1.3 83.7 + - + -
1286B THR 3.7 0.2 - - - -
1288B ASN* 4.7 2.1 + - - +
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Residues in contact with HIS1285 (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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542B TYR* 5.1 1.6 + - - -
992B CYS* 2.9 52.2 + - - -
993B TRP* 3.4 32.8 - + - -
1166B CYS* 6.0 1.4 - - - +
1281B ALA* 3.0 10.4 + - - +
1284B GLN* 1.3 92.4 - - + +
1286B THR* 1.3 62.2 + - - +
1288B ASN* 5.4 1.3 - - - -
1310B VAL* 3.6 17.5 - - - +
1311B ASP* 4.1 17.8 - - + +
1312B LYS* 5.5 4.0 - - + +
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Residues in contact with THR1286 (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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1282B ARG* 2.5 44.3 + - - +
1284B GLN 3.7 0.2 - - - -
1285B HIS* 1.3 72.7 - - - +
1287B ASN* 1.3 86.2 + - - +
1288B ASN* 2.6 40.3 + - - +
1310B VAL* 2.7 51.4 + - + +
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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
------------------------------------------------------------
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