Contacts of the strand formed by residues 1314 - 1321 (chain B) in PDB entry 3PT6
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 ARG1314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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705B ASP* 4.4 8.3 + - - +
706B GLU 4.0 16.4 + - - -
707B GLU* 5.3 3.6 - - - +
709B ASP* 3.4 25.6 + - - -
1271B VAL* 4.2 0.2 - - - -
1272B ARG* 3.1 60.8 + - + +
1273B ASN* 5.6 0.8 + - - -
1301B VAL* 4.3 8.5 - - + -
1302B LEU 3.1 9.6 - - - +
1303B GLN* 3.7 20.6 - - + +
1312B THR* 5.4 2.0 - - - +
1313B ARG* 1.3 74.4 - - - +
1315B ARG* 1.3 69.5 + - - +
1341B ALA* 3.8 18.2 - - - +
1343B GLN* 3.3 31.9 + - - +
1344B LEU* 5.1 1.1 - - + -
1527B THR* 5.4 0.2 - - - +
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Residues in contact with ARG1315 (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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1269B GLU* 2.6 38.5 + - - +
1270B ASN* 3.0 20.9 - - - +
1271B VAL* 3.4 36.2 - - - +
1272B ARG* 4.5 2.7 - - - -
1301B VAL* 3.4 4.1 - - - -
1302B LEU* 2.9 34.1 + - + +
1313B ARG* 3.9 45.7 - - + +
1314B ARG* 1.3 83.6 + - - +
1316B ALA* 1.3 60.2 + - - +
1317B ILE* 3.8 7.0 + - + +
1527B THR* 5.4 2.2 - - - +
1580B ASN 5.4 3.8 + - - -
1581B ALA 5.8 0.6 + - - -
1582B VAL* 4.5 9.5 - - - +
1583B PRO* 4.9 2.5 - - - -
1586B LEU* 4.6 20.6 - - + -
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Residues in contact with ALA1316 (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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1268B LEU* 4.0 1.2 - - - +
1269B GLU* 3.6 1.0 - - - -
1270B ASN* 2.8 32.2 + - - +
1271B VAL 3.0 16.2 + - - +
1272B ARG* 4.1 4.9 - - - +
1274B PHE* 4.3 13.2 - - + -
1275B VAL* 3.6 30.5 - - + -
1299B PHE* 6.1 0.2 - - + -
1300B GLY 3.4 8.1 - - - +
1301B VAL* 4.3 2.9 - - + -
1315B ARG* 1.3 72.3 - - - +
1317B ILE* 1.3 62.4 - - - +
1318B ILE* 5.1 3.4 - - + +
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Residues in contact with ILE1317 (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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1267B LEU* 4.1 7.2 - - + -
1268B LEU 3.4 6.5 - - - +
1269B GLU* 4.4 12.1 - - + -
1299B PHE* 3.4 1.4 - - - +
1300B GLY 3.1 26.7 + - - +
1302B LEU* 3.8 21.5 - - + -
1315B ARG* 3.8 13.4 + - + +
1316B ALA* 1.3 79.0 - - - +
1318B ILE* 1.3 64.0 + - - +
1319B LEU* 3.8 20.6 - - + -
1330B PHE* 3.4 36.6 - - + -
1331B PRO* 5.5 1.3 - - + -
1586B LEU* 5.8 3.1 - - + -
1590B ILE* 3.9 26.9 - - + -
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Residues in contact with ILE1318 (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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1266B PHE* 3.8 10.3 - - + +
1267B LEU* 3.6 5.2 - - - +
1268B LEU* 2.9 48.0 + - + +
1274B PHE* 4.4 24.5 - - + -
1275B VAL* 6.3 0.2 - - + -
1283B LEU* 4.5 7.0 - - + -
1286B THR* 4.9 6.5 - - - +
1287B LEU* 4.9 4.0 - - + -
1290B LEU* 3.2 35.7 - - + -
1298B THR 3.4 16.4 - - - +
1299B PHE* 4.0 11.4 - - + -
1316B ALA* 5.1 3.6 - - + -
1317B ILE* 1.3 79.6 - - - +
1319B LEU* 1.3 70.4 + - - +
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Residues in contact with LEU1319 (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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1266B PHE 3.5 4.0 - - - +
1267B LEU* 3.6 32.8 - - + -
1297B CYS* 3.0 5.7 - - - +
1298B THR* 2.9 38.8 + - + +
1317B ILE* 3.8 14.1 - - + -
1318B ILE* 1.3 75.3 - - - +
1320B ALA* 1.3 61.1 + - - +
1327B LEU* 3.6 7.0 - - + +
1328B PRO* 4.0 31.4 - - + +
1329B LEU 4.3 5.4 - - - +
1330B PHE* 3.4 36.8 - - + -
1590B ILE* 4.7 11.2 - - + -
1593B GLU* 6.3 0.4 - - + -
1594B ILE* 5.8 5.2 - - + -
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Residues in contact with ALA1320 (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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1265B PHE* 3.6 5.7 - - - +
1266B PHE* 3.0 55.3 + - + +
1290B LEU* 4.0 13.5 - - + -
1295B TYR* 3.7 17.5 - - + -
1296B GLN 3.1 9.6 - - - +
1297B CYS* 4.3 3.1 - - + -
1319B LEU* 1.3 78.6 - - - +
1321B ALA* 1.3 65.8 + - - +
1327B LEU* 4.3 1.1 - - - -
1328B PRO* 4.9 1.7 - - - +
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Residues in contact with ALA1321 (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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1264B ARG 3.4 11.9 - - - +
1265B PHE* 4.0 15.7 - - + -
1295B TYR* 3.5 5.3 - - - -
1296B GLN* 2.8 34.4 + - - +
1320B ALA* 1.3 79.9 - - - +
1322B ALA* 1.3 71.9 + - - +
1325B GLU* 4.3 2.9 - - + -
1327B LEU* 4.0 29.8 - - + +
1328B PRO* 4.6 0.4 - - + -
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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
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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