Contacts of the strand formed by residues 1296 - 1303 (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 GLN1296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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871A LEU* 4.2 4.0 - - + -
880A PHE 3.1 16.4 - - - +
881A GLU* 3.5 10.0 - - - +
882A SER* 2.9 46.5 + - - +
1294A GLY 5.2 0.2 - - - +
1295A TYR* 1.3 74.0 - - - +
1297A CYS* 1.3 59.5 + - - +
1320A ALA* 3.0 4.3 - - - -
1321A ALA* 2.8 37.0 + - + +
1322A ALA 3.2 8.6 + - - +
1323A PRO* 3.1 12.0 + - + -
1325A GLU* 2.8 29.2 + - - +
1326A LYS* 4.7 0.2 - - - -
1327A LEU* 3.7 27.3 + - + +
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Residues in contact with CYS1297 (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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879A ARG* 3.7 0.7 - - - -
880A PHE* 2.9 48.2 + - - -
1287A LEU* 3.5 30.1 - - + -
1290A LEU* 3.9 33.2 - - + -
1291A VAL* 4.7 4.0 - - - -
1295A TYR 4.4 5.8 - - - -
1296A GLN* 1.3 76.2 - - - +
1298A THR* 1.3 62.8 + - - +
1319A LEU 3.1 13.5 - - - +
1320A ALA* 4.3 1.6 - - + -
1327A LEU* 3.8 6.4 - - - +
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Residues in contact with THR1298 (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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877A TYR 3.3 12.0 + - - -
878A ALA 3.1 18.9 + - - -
879A ARG* 3.5 22.7 - - - +
1287A LEU* 4.8 5.2 - - - -
1297A CYS* 1.3 76.1 - - - +
1299A PHE* 1.3 74.5 + - - +
1318A ILE* 3.4 7.1 - - - +
1319A LEU* 2.9 37.9 + - + +
1327A LEU* 3.9 14.4 - - + -
1328A PRO 4.6 1.3 - - - +
1330A PHE* 3.7 22.6 - - + -
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Residues in contact with PHE1299 (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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807A VAL* 3.9 17.5 - - + -
877A TYR 4.3 5.9 - - - +
878A ALA* 3.4 26.9 - - + -
1275A VAL* 4.8 8.1 - - + -
1283A LEU* 3.7 31.9 - - + -
1287A LEU* 3.9 19.7 - - + -
1298A THR* 1.3 87.8 + - - +
1300A GLY* 1.3 63.6 + - - +
1317A ILE 3.1 13.5 - - - +
1318A ILE* 4.1 17.0 - - + -
1330A PHE* 3.5 8.9 - - - -
1346A VAL* 3.7 28.3 - - + -
1348A VAL* 4.6 2.0 - - + -
1353A PHE* 4.1 25.8 - + + -
1354A VAL 5.3 1.4 - - - +
1355A SER* 4.9 5.0 - - - -
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Residues in contact with GLY1300 (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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1299A PHE* 1.3 85.2 - - - +
1301A VAL* 1.3 63.1 - - - -
1316A ALA* 3.5 2.3 - - - +
1317A ILE* 2.8 35.8 + - - +
1330A PHE* 3.3 17.3 - - - -
1346A VAL* 5.6 2.5 - - - -
1354A VAL 6.2 0.4 - - - -
1355A SER* 4.7 9.2 - - - -
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Residues in contact with VAL1301 (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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1272A ARG* 3.7 35.2 - - + +
1275A VAL* 4.3 22.2 - - + -
1300A GLY* 1.3 78.1 - - - +
1302A LEU* 1.3 80.4 + - - +
1314A ARG* 4.1 11.0 - - + -
1315A ARG 3.3 11.2 - - - +
1316A ALA* 4.5 1.3 - - - -
1343A GLN 4.7 1.3 - - - +
1344A LEU* 3.7 49.0 + - + +
1346A VAL* 4.5 12.1 - - + -
1355A SER* 5.0 3.9 + - - -
1357A ILE* 4.8 1.6 - - - +
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Residues in contact with LEU1302 (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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1301A VAL* 1.3 83.5 - - - +
1303A GLN* 1.3 60.3 + - - +
1304A ALA 4.0 0.2 - - - -
1307A TYR* 3.5 22.9 - - + +
1313A ARG 3.4 1.4 - - - +
1314A ARG* 3.1 5.5 - - - +
1315A ARG* 2.9 32.9 + - - +
1317A ILE* 3.9 19.3 - - + -
1330A PHE* 3.6 30.7 - - + -
1331A PRO* 3.9 15.0 - - + -
1344A LEU* 4.3 4.5 - - + -
1355A SER* 5.2 0.2 - - - +
1357A ILE* 3.6 18.8 - - + -
1586A LEU* 4.2 23.2 - - + +
1590A ILE* 4.3 15.9 - - + -
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Residues in contact with GLN1303 (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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1302A LEU* 1.3 74.8 - - - +
1304A ALA* 1.3 68.0 + - - +
1305A GLY* 2.7 28.8 - - - +
1306A GLN* 3.2 43.5 + - + +
1307A TYR* 3.5 9.2 - - - -
1311A GLN 3.2 7.7 + - - -
1312A THR* 3.4 16.8 - - - +
1313A ARG 3.1 22.6 + - - +
1314A ARG* 3.6 7.0 - - + +
1337A PHE* 3.5 17.1 - - + -
1341A ALA 2.7 30.5 - - - +
1342A CYS* 4.0 1.3 - - - -
1344A LEU* 4.0 12.4 - - + +
1586A LEU* 4.6 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