Contacts of the strand formed by residues 1297 - 1304 (chain B) in PDB entry 2VK7
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 ILE1297 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1283B ASP* 3.5 28.7 - - + -
1284B ALA 3.4 8.1 - - - +
1285B ARG* 3.7 32.8 - - + +
1290B ALA 4.1 4.9 - - - +
1292B ALA 4.0 22.0 - - - +
1295B ASN* 3.8 11.4 - - + -
1296B ASP* 1.3 77.9 + - - +
1298B ASP* 1.3 70.5 + - - +
1320B TYR 5.2 1.2 + - - -
1324B SER 4.2 2.3 - - - +
1325B SER* 3.0 23.8 + - - +
1326B VAL* 3.1 43.1 + - - +
1327B ILE* 4.1 10.3 - - + -
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Residues in contact with ASP1298 (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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1283B ASP* 3.6 5.5 - - - -
1284B ALA* 2.8 35.5 + - + +
1286B ARG* 2.8 42.3 + - - +
1297B ILE* 1.3 78.7 - - - +
1299B THR* 1.3 62.5 + - - +
1316B ILE* 3.9 11.9 - - + -
1318B MET 3.3 10.5 - - - +
1319B ASP* 3.1 19.8 - - - +
1326B VAL* 3.8 3.1 - - - -
2694B CA 2.4 30.1 - - - -
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Residues in contact with THR1299 (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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1281B SER* 4.8 0.9 - - - -
1282B ILE 3.6 6.5 - - - +
1283B ASP* 5.0 1.1 + - - +
1298B ASP* 1.3 73.2 - - - +
1300B ALA* 1.3 67.0 - - - +
1316B ILE* 3.3 6.3 - - - +
1317B ILE* 2.8 54.5 + - + -
1318B MET* 3.0 23.7 + - + +
1326B VAL* 3.3 22.4 + - - +
1329B THR* 3.7 30.5 - - + +
1342B LEU* 4.4 7.2 - - + -
1344B VAL* 4.0 0.7 - - - +
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Residues in contact with ALA1300 (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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1255B PHE* 4.5 3.1 - - + -
1260B LEU* 3.9 14.1 - - + -
1265B TYR* 4.4 9.0 - - + -
1281B SER* 3.2 5.9 - - - -
1282B ILE* 3.0 50.6 + - + +
1284B ALA* 4.4 2.5 - - + -
1298B ASP 4.0 0.8 + - - -
1299B THR* 1.3 72.4 - - - +
1301B VAL* 1.3 65.7 + - - +
1315B GLN 3.3 10.1 - - - +
1316B ILE* 3.8 16.4 - - + -
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Residues in contact with VAL1301 (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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1255B PHE* 4.7 1.3 - - - -
1279B ILE* 3.6 26.2 - - + -
1280B ALA 3.2 4.3 - - - +
1281B SER* 4.0 5.6 - - - -
1299B THR* 4.7 0.4 - - + -
1300B ALA* 1.3 81.1 - - - +
1302B ARG* 1.3 71.1 + - - +
1303B ARG* 4.6 8.1 - - + -
1312B ASP* 4.3 0.9 - - - +
1314B GLY* 3.2 4.2 - - - -
1315B GLN* 2.9 44.1 + - + +
1317B ILE* 3.7 31.9 - - + -
1342B LEU* 3.8 15.5 - - + -
1440B GLY 4.8 0.7 - - - +
1443B TRP* 4.4 15.0 - - + +
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Residues in contact with ARG1302 (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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1253B ASP 4.5 3.4 + - - -
1254B LEU* 2.8 54.1 + - + +
1255B PHE* 3.6 19.7 - - + -
1256B HIS* 5.3 2.4 - - - -
1259B PHE* 3.3 38.0 - - + -
1278B LEU 3.8 0.2 - - - +
1279B ILE* 3.5 3.3 - - - -
1280B ALA 2.8 32.6 + - - +
1301B VAL* 1.3 79.4 - - - +
1303B ARG* 1.3 63.5 + - - +
1311B TRP* 3.5 38.6 + - + +
1312B ASP* 2.8 30.6 + - - +
1313B GLU* 4.7 4.4 + - - -
1314B GLY* 3.9 4.9 - - - -
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Residues in contact with ARG1303 (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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1277B THR* 3.6 10.6 + - + +
1278B LEU 3.2 6.7 - - - +
1279B ILE* 4.5 12.1 - - + -
1301B VAL* 4.6 5.6 - - + -
1302B ARG* 1.3 78.1 - - - +
1304B SER* 1.3 60.4 + - - +
1305B GLU* 2.8 35.7 + - - +
1311B TRP* 3.4 5.7 - - - -
1312B ASP* 2.9 51.4 + - + +
1315B GLN* 5.0 3.1 - - - +
1439B ASP* 3.0 44.7 + - - -
1440B GLY 3.4 24.8 - - - +
1441B LYS* 3.6 29.3 - - - +
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Residues in contact with SER1304 (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 GLY 4.5 0.5 - - - +
1277B THR* 3.4 6.7 - - - +
1278B LEU* 2.9 36.2 + - - +
1303B ARG* 1.3 74.5 - - - +
1305B GLU* 1.3 62.1 + - - +
1306B ASP* 2.9 7.4 + - - -
1307B GLY 4.7 0.2 + - - -
1308B GLY* 2.9 30.9 + - - -
1310B THR 2.7 25.3 + - - -
1311B TRP* 3.6 21.1 - - - -
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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