Contacts of the helix formed by residues 1366 - 1372 (chain A) in PDB entry 4YOC
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 THR1366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1307A ALA* 3.6 4.5 - - - -
1363A ARG* 4.6 3.4 - - - +
1364A THR* 4.1 17.0 - - + +
1365A ILE* 1.3 78.4 - - - +
1367A VAL* 1.3 55.8 + - - +
1368A ARG* 3.5 7.6 + - - +
1369A ASP* 2.9 36.9 + - - +
1370A THR* 2.6 36.4 + - - -
1519A TRP 3.4 11.5 + - - -
1520A ASP* 3.6 22.0 - - - +
1521A GLY 3.5 7.2 - - - +
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Residues in contact with VAL1367 (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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1307A ALA* 4.8 0.2 - - - -
1366A THR* 1.3 73.3 - - - +
1368A ARG* 1.3 59.8 + - - +
1370A THR* 2.9 8.2 + - - -
1371A MET* 2.9 59.8 + - + +
1517A LEU* 4.4 9.6 - - + -
1518A GLU 3.2 26.0 - - - +
1519A TRP* 3.5 12.9 + - + +
1521A GLY 3.1 16.3 + - - +
1522A PHE* 3.9 11.9 - - - +
1523A PHE* 4.0 18.6 - - + -
1542A PRO* 4.1 7.0 - - + -
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Residues in contact with ARG1368 (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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1035A TYR* 3.4 59.9 + - - -
1366A THR* 3.6 5.4 + - - +
1367A VAL* 1.3 77.7 - - - +
1369A ASP* 1.3 65.2 + - - +
1370A THR 3.2 0.5 + - - -
1372A SER* 3.0 42.9 + - - +
1393A GLN* 6.0 0.7 - - - +
1394A SER* 5.2 0.5 - - - -
1397A GLN* 3.3 0.2 + - - -
1519A TRP* 3.0 52.4 + - + +
1520A ASP* 2.3 37.4 + - - -
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Residues in contact with ASP1369 (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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1035A TYR* 4.4 9.7 - - - +
1363A ARG* 2.7 47.8 + - - +
1365A ILE* 3.5 14.8 - - + +
1366A THR* 2.9 33.7 + - - +
1368A ARG* 1.3 81.5 - - - +
1370A THR* 1.3 56.5 + - - +
1394A SER* 2.9 32.4 + - - +
1396A PHE* 3.5 15.3 - - + -
1397A GLN* 3.2 13.2 - - - +
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Residues in contact with THR1370 (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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1307A ALA* 4.0 12.5 + - - +
1365A ILE* 4.2 2.9 - - - +
1366A THR 2.6 19.5 + - - -
1367A VAL* 2.9 13.6 + - - -
1369A ASP* 1.3 79.9 - - - +
1371A MET* 1.3 63.0 + - + +
1372A SER 4.0 0.2 - - - -
1396A PHE* 3.7 14.5 - - + -
1397A GLN* 4.2 0.6 - - - +
1523A PHE* 4.5 8.7 - - + -
1552A GLU 4.3 3.6 - - - +
1555A ARG* 2.8 66.3 + - + +
1556A SER* 3.7 7.9 - - - +
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Residues in contact with MET1371 (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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1367A VAL* 2.9 37.6 + - + +
1370A THR* 1.3 81.1 - - + +
1372A SER* 1.3 65.0 + - - +
1373A ASP* 3.2 3.7 + - - -
1374A LEU* 3.6 19.6 + - + +
1517A LEU* 4.1 12.6 - - + -
1519A TRP* 4.3 8.9 - - + -
1523A PHE* 3.8 17.0 - - - -
1541A HIS* 3.9 17.4 + - + +
1542A PRO* 3.6 25.4 - - + -
1548A VAL* 4.2 4.9 - - + -
1552A GLU* 3.5 43.1 - - + +
1555A ARG* 4.0 7.6 - - + +
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Residues in contact with SER1372 (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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1367A VAL 4.3 0.4 + - - -
1368A ARG* 3.0 31.8 + - - +
1371A MET* 1.3 77.3 - - - +
1373A ASP* 1.3 59.7 + - - +
1374A LEU 3.3 4.0 + - - +
1393A GLN* 3.0 32.2 + - - +
1394A SER* 5.5 0.7 - - - -
1397A GLN* 2.9 19.5 + - - +
1519A TRP* 4.2 14.8 - - - -
854C ARG* 4.8 2.9 + - - -
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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