Contacts of the helix formed by residues 1331 - 1336 (chain A) in PDB entry 5W0N
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 ASP1331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1327A GLU 3.5 18.8 + - - +
1328A TYR* 3.7 9.6 + - - +
1329A PHE 3.4 3.8 + - - -
1330A PHE* 1.3 75.2 - - - +
1332A PRO* 1.3 73.0 - - - +
1333A ASP* 3.1 22.1 + - - +
1334A VAL* 3.1 27.3 + - + +
1335A LEU* 3.0 23.3 + - - +
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Residues in contact with PRO1332 (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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1157A MET* 3.8 41.7 - - + +
1330A PHE 3.2 7.8 - - - +
1331A ASP* 1.3 91.0 - - - +
1333A ASP* 1.3 59.2 + - - +
1335A LEU* 4.4 7.0 - - + +
1336A THR* 2.7 43.5 + - + +
1338A GLY* 5.4 0.2 - - - -
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Residues in contact with ASP1333 (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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1331A ASP* 3.1 16.1 + - - +
1332A PRO* 1.3 80.6 - - - +
1334A VAL* 1.3 59.4 + - + +
1337A GLU* 3.1 22.5 - - - -
1338A GLY* 3.2 19.6 + - - +
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Residues in contact with VAL1334 (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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1306A ASN* 3.5 13.5 + - - -
1309A ARG* 4.0 13.4 + - - +
1310A VAL* 3.5 30.5 - - + -
1328A TYR 5.6 2.2 - - - +
1331A ASP* 3.1 31.7 + - + +
1332A PRO 3.1 0.4 - - - -
1333A ASP* 1.3 80.4 - - + +
1335A LEU* 1.3 64.3 + - + +
1336A THR 3.3 0.9 + - - -
1337A GLU* 3.5 10.0 + - - +
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Residues in contact with LEU1335 (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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1154A PHE* 3.8 23.1 - - + -
1157A MET* 5.1 5.4 - - + -
1158A CYS* 3.8 22.0 - - - -
1303A ALA* 3.5 15.1 - - - +
1306A ASN* 2.8 23.5 + - - +
1307A GLY* 3.7 33.4 - - - +
1310A VAL* 3.9 18.8 - - + -
1311A PHE* 5.1 0.4 - - + -
1329A PHE 3.9 20.4 - - - +
1330A PHE* 3.9 18.2 - - + +
1331A ASP 3.0 16.6 + - - +
1332A PRO* 4.3 4.3 - - + +
1334A VAL* 1.3 77.4 - - + +
1336A THR* 1.3 58.3 + - - +
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Residues in contact with THR1336 (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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1157A MET 5.3 0.9 - - - +
1158A CYS* 3.9 32.5 - - + +
1299A PHE* 3.6 28.5 - - + +
1302A LYS* 6.5 0.7 - - - -
1303A ALA* 4.7 3.4 - - + +
1306A ASN* 4.4 0.9 - - - +
1332A PRO* 2.7 25.3 + - + +
1335A LEU* 1.3 81.2 - - + +
1337A GLU* 1.3 71.5 + - - +
1338A GLY* 3.9 3.3 + - - -
1339A GLU* 3.1 36.6 + - - +
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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