Contacts of the helix formed by residues 1318 - 1324 (chain A) in PDB entry 6CNB
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 HIS1318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1125A ARG* 3.9 6.5 - - - +
1129A ILE* 5.7 2.8 - - - +
1133A SER 5.5 4.7 - - - +
1134A LYS 5.1 9.2 - - - +
1136A ILE* 3.5 35.4 - - + -
1139A PRO* 3.9 21.6 - - + +
1141A ILE* 4.4 2.9 - - + -
1297A GLY 4.3 10.1 - - - -
1298A TYR* 4.0 18.2 + + - -
1316A THR* 3.2 17.2 + - - -
1317A ASN* 1.3 95.3 + - - +
1319A VAL* 1.3 67.9 + - - +
1320A LEU* 2.9 7.2 + - + -
1321A GLU* 3.1 43.4 + - + +
1322A VAL 3.8 1.9 + - - -
1338A GLU* 4.4 2.0 + - - -
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Residues in contact with VAL1319 (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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1129A ILE* 4.6 12.9 - - + +
1132A ALA* 5.9 3.8 - - + -
1317A ASN 3.6 2.4 - - - -
1318A HIS* 1.3 71.0 - - - +
1320A LEU* 1.3 64.0 + - - +
1322A VAL* 2.8 20.8 + - - +
1323A PHE* 2.9 10.0 + - - +
1331A ALA* 3.6 34.3 - - + +
1334A SER* 4.8 5.2 - - - +
1335A ILE* 3.8 42.8 - - + +
1338A GLU* 4.7 10.5 - - - +
1368A VAL* 4.2 19.5 - - + -
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Residues in contact with LEU1320 (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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1132A ALA* 5.1 12.1 - - + +
1133A SER 4.1 14.6 - - - +
1134A LYS* 3.8 52.0 - - + +
1318A HIS* 2.9 3.2 + - + +
1319A VAL* 1.3 78.3 - - - +
1321A GLU* 1.3 59.3 + - - +
1323A PHE* 2.9 45.5 + - + +
1324A SER* 3.3 7.8 + - - -
1368A VAL* 4.7 18.3 - - + +
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Residues in contact with GLU1321 (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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1298A TYR* 3.3 23.1 - - + +
1299A GLY 2.7 24.6 - - - +
1300A LEU* 3.1 27.8 - - - +
1316A THR* 4.5 0.3 - - - +
1318A HIS* 3.1 36.2 + - + +
1320A LEU* 1.3 76.7 - - - +
1322A VAL* 1.3 65.4 + - - +
1324A SER* 3.2 18.1 + - - +
1325A VAL* 3.3 17.5 + - - +
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Residues in contact with VAL1322 (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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1300A LEU* 3.7 5.6 - - + -
1316A THR* 3.4 33.2 - - + -
1317A ASN 4.4 5.2 - - - +
1318A HIS 3.8 0.4 + - - +
1319A VAL* 2.8 15.2 + - - +
1321A GLU* 1.3 78.4 - - - +
1323A PHE* 1.3 62.7 + - - +
1324A SER 3.0 1.4 + - - -
1325A VAL* 3.0 17.7 + - + -
1326A LEU* 3.0 29.2 + - + -
1327A GLY 3.1 4.2 + - - -
1330A ALA* 4.3 5.2 - - + +
1331A ALA* 3.8 28.0 - - - +
1334A SER* 5.1 11.9 - - - +
149E LEU* 5.2 6.7 - - + -
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Residues in contact with PHE1323 (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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1319A VAL 2.9 8.8 + - - +
1320A LEU* 2.9 29.2 + - + +
1322A VAL* 1.3 76.7 - - - +
1324A SER* 1.3 61.3 + - - +
1325A VAL 3.4 0.2 - - - -
1327A GLY* 3.3 18.7 - - - -
1328A ILE* 3.2 36.1 - - + -
1331A ALA* 4.0 8.9 - - + +
1366A GLY 3.3 19.7 - - - -
1367A GLU* 3.5 26.9 - - + -
1368A VAL* 3.7 20.6 - - + -
179E GLN* 3.6 15.5 - - + -
182E ASP* 4.3 9.4 - - - +
183E PRO* 4.8 2.6 - - - +
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Residues in contact with SER1324 (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 ARG* 3.1 18.2 + - - -
1320A LEU* 3.3 9.1 + - - -
1321A GLU* 3.2 15.6 + - - -
1322A VAL 3.0 1.6 + - - -
1323A PHE* 1.3 81.7 - - - +
1325A VAL* 1.3 60.9 + - - +
183E PRO* 4.8 7.5 - - - +
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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