Contacts of the helix formed by residues 1303 - 1310 (chain A) in PDB entry 5XA0
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 GLY1303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1300A GLU* 3.2 7.6 + - - -
1302A HIS* 1.4 74.1 - - - +
1304A ARG* 1.3 65.5 + - - +
1305A ASN* 3.1 3.6 - - - -
1306A VAL* 3.0 23.9 + - - +
1307A GLN 4.3 0.5 + - - -
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Residues in contact with ARG1304 (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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1297A HIS* 5.6 1.8 - - + -
1300A GLU* 2.8 36.3 - - + +
1301A THR 5.9 0.2 - - - -
1302A HIS 3.5 2.7 - - - -
1303A GLY* 1.3 73.9 - - - +
1305A ASN* 1.3 65.8 + - - +
1306A VAL 2.9 1.7 + - - -
1307A GLN* 3.1 20.0 + - - +
1308A TYR* 4.1 2.3 + - - +
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Residues in contact with ASN1305 (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 HIS 4.9 5.5 + - - +
1303A GLY* 3.0 2.5 + - - -
1304A ARG* 1.3 78.9 - - - +
1306A VAL* 1.3 65.0 + - - +
1308A TYR* 3.0 9.5 + - - +
1309A ILE* 2.8 25.7 + - + +
1358A MET* 6.5 1.1 - - + -
1361A GLU* 5.7 5.8 - - + -
1362A ARG* 5.0 19.7 - - + +
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Residues in contact with VAL1306 (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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1303A GLY* 3.0 15.2 + - - +
1304A ARG 2.9 0.4 + - - -
1305A ASN* 1.3 77.3 - - - +
1307A GLN* 1.3 53.7 + - - +
1309A ILE* 2.9 7.9 + - - -
1310A LYS* 2.1 47.8 + - + +
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Residues in contact with GLN1307 (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* 6.1 0.7 - - - +
1303A GLY 4.3 0.4 + - - -
1304A ARG* 3.1 11.3 + - - +
1306A VAL* 1.3 77.9 - - - +
1308A TYR* 1.3 58.7 + - - +
1310A LYS* 3.4 23.1 - - - +
1311A PHE 4.0 5.2 - - - +
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Residues in contact with TYR1308 (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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1304A ARG 4.1 1.5 + - - +
1305A ASN* 3.0 10.5 + - - +
1307A GLN* 1.3 76.6 - - - +
1309A ILE* 1.3 64.7 + - - +
1310A LYS 3.0 1.9 + - - -
1312A LEU* 3.7 32.2 + - + +
1365A MET* 5.7 1.8 - - - +
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Residues in contact with ILE1309 (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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1305A ASN* 2.8 21.8 + - + +
1306A VAL* 3.7 6.7 - - - +
1308A TYR* 1.3 73.8 - - - +
1310A LYS* 1.3 54.8 + - - +
1311A PHE 3.1 6.7 + - - -
1364A ARG* 4.6 25.1 - - + +
1365A MET* 5.1 10.1 - - + -
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Residues in contact with LYS1310 (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 ILE* 5.6 3.5 - - - +
1306A VAL* 2.1 39.7 + - + +
1307A GLN* 3.4 13.4 - - - +
1308A TYR 3.0 0.6 - - - -
1309A ILE* 1.3 65.6 - - - +
1311A PHE* 1.3 72.7 + - - +
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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