Contacts of the strand formed by residues 1314 - 1321 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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705A ASP* 6.3 0.4 - - - +
706A GLU 4.2 4.8 + - - -
707A GLU* 4.1 19.4 - - - +
709A ASP* 3.4 25.6 + - - -
1272A ARG* 3.3 62.8 + - + +
1301A VAL* 4.1 6.3 - - + -
1302A LEU 3.1 8.5 - - - +
1303A GLN* 3.6 20.0 - - + +
1312A THR* 5.2 5.0 - - + +
1313A ARG* 1.3 71.2 - - - +
1315A ARG* 1.3 74.9 + - - +
1340A ARG 5.8 1.1 + - - -
1341A ALA* 3.7 16.1 - - - +
1343A GLN* 2.8 35.6 + - - +
1344A LEU* 4.9 2.0 - - - -
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Residues in contact with ARG1315 (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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1269A GLU* 3.0 29.5 + - - +
1270A ASN* 3.1 20.2 + - - +
1271A VAL* 3.5 35.8 - - - +
1272A ARG* 4.0 4.0 - - - +
1300A GLY 3.8 0.2 - - - +
1301A VAL* 3.3 4.2 - - - -
1302A LEU* 2.9 30.8 + - + +
1313A ARG* 3.8 52.0 - - + +
1314A ARG* 1.3 88.2 + - - +
1316A ALA* 1.3 62.5 + - - +
1317A ILE* 3.9 11.7 - - + +
1527A THR* 5.9 2.2 - - - +
1580A ASN 5.6 1.8 + - - -
1582A VAL* 4.8 4.1 - - - +
1583A PRO* 4.7 5.4 - - - -
1586A LEU* 4.5 19.7 - - + -
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Residues in contact with ALA1316 (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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1268A LEU* 4.6 0.4 - - - -
1269A GLU* 3.5 0.3 - - - -
1270A ASN* 3.0 28.9 + - + +
1271A VAL 3.4 19.5 + - - +
1272A ARG* 3.9 2.2 - - - +
1274A PHE* 3.9 14.4 - - + -
1275A VAL* 3.4 31.2 - - + -
1300A GLY 3.5 5.8 - - - +
1301A VAL* 4.5 2.9 - - + +
1315A ARG* 1.3 72.3 - - - +
1317A ILE* 1.3 68.0 + - - +
1318A ILE* 5.0 3.6 - - + -
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Residues in contact with ILE1317 (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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1267A LEU* 3.5 21.1 - - + -
1268A LEU 3.5 2.2 - - - -
1269A GLU* 3.7 20.0 - - + -
1299A PHE* 3.1 7.1 - - - +
1300A GLY 2.8 36.3 + - - +
1302A LEU* 3.9 20.9 - - + -
1315A ARG* 3.9 18.4 - - + +
1316A ALA* 1.3 89.2 - - - +
1318A ILE* 1.3 66.7 + - - +
1319A LEU* 4.0 14.6 - - + -
1330A PHE* 3.8 14.4 - - + -
1586A LEU* 5.2 6.1 - - + -
1590A ILE* 4.1 22.2 - - + -
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Residues in contact with ILE1318 (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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1266A PHE* 3.8 13.5 - - + -
1267A LEU* 3.3 12.6 - - - +
1268A LEU* 2.8 45.1 + - + +
1274A PHE* 4.1 28.9 - - + -
1275A VAL* 6.1 0.7 - - + -
1283A LEU* 4.3 7.2 - - + -
1286A THR* 4.4 13.7 - - - +
1287A LEU* 5.0 4.0 - - + -
1290A LEU* 3.7 29.2 - - + -
1297A CYS* 5.1 0.7 - - + -
1298A THR 3.4 4.5 - - - +
1299A PHE* 4.1 16.2 - - + -
1316A ALA* 5.0 2.0 - - + -
1317A ILE* 1.3 85.9 - - - +
1319A LEU* 1.3 69.7 + - - +
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Residues in contact with LEU1319 (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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1266A PHE 3.6 3.6 - - - +
1267A LEU* 4.0 22.0 - - + -
1297A CYS* 3.1 7.8 - - - +
1298A THR* 2.9 40.6 + - + +
1317A ILE* 4.0 6.9 - - + -
1318A ILE* 1.3 86.4 - - - +
1320A ALA* 1.3 61.5 + - - +
1327A LEU* 4.1 8.3 - - + -
1328A PRO* 3.8 36.8 - - + +
1329A LEU 3.9 13.0 - - - +
1330A PHE* 4.2 24.0 - - + -
1590A ILE* 4.6 15.7 - - + -
1594A ILE* 5.3 6.5 - - + -
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Residues in contact with ALA1320 (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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1265A PHE* 3.7 9.5 - - - -
1266A PHE* 3.0 54.6 + - + +
1290A LEU* 4.0 13.0 - - + -
1295A TYR* 3.9 13.0 - - + -
1296A GLN 3.0 11.2 - - - +
1297A CYS* 4.4 2.0 - - + -
1319A LEU* 1.3 77.1 - - - +
1321A ALA* 1.3 64.6 + - - +
1327A LEU* 4.2 2.8 - - - +
1328A PRO* 4.8 1.6 - - - +
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Residues in contact with ALA1321 (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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1264A ARG 3.3 6.7 - - - +
1265A PHE* 4.4 5.4 - - + -
1295A TYR* 3.3 7.4 - - - -
1296A GLN* 2.8 35.7 + - + +
1320A ALA* 1.3 77.5 - - - +
1322A ALA* 1.3 69.3 + - - +
1325A GLU* 3.8 19.7 - - + -
1326A LYS 4.0 2.7 - - - +
1327A LEU* 4.0 28.5 - - + +
1328A PRO* 4.4 0.2 - - + -
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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