Contacts of the helix formed by residues 1297 - 1303 (chain A) in PDB entry 2XBA
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 PRO1297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1295A TRP 4.1 2.5 - - - +
1296A MET* 1.3 91.9 - - + +
1298A PRO* 1.3 78.8 - - + +
1299A GLU* 3.3 26.7 - - - +
1300A ALA* 3.0 22.9 + - + +
1301A PHE* 3.5 7.3 + - - -
1306A PHE* 5.9 0.4 - - + -
1310A THR* 3.4 31.0 - - + +
1313A TRP* 3.5 28.7 - - + -
1314A SER* 4.8 0.4 - - - +
1373A ARG* 3.6 7.6 - - - +
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Residues in contact with PRO1298 (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 PRO* 1.3 89.8 - - + +
1299A GLU* 1.3 66.4 + - - +
1301A PHE* 3.2 15.4 + - + +
1302A MET* 3.0 33.7 + - - +
1313A TRP* 3.6 23.3 - - + -
1342A VAL* 3.8 22.0 - - + +
1343A THR* 4.2 12.6 - - + -
1347A ARG* 4.8 0.4 - - - +
1368A HIS* 3.8 36.1 - - + +
1373A ARG* 4.0 2.0 - - - +
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Residues in contact with GLU1299 (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 PRO* 3.3 8.7 - - - +
1298A PRO* 1.3 76.2 - - - +
1300A ALA* 1.3 61.7 + - - +
1301A PHE 3.4 0.2 - - - -
1302A MET* 4.6 7.9 - - - -
1303A GLU* 3.2 22.9 + - + +
1304A GLY 3.3 5.2 + - - -
1305A ILE* 3.4 30.8 + - + +
1307A THR* 5.2 1.3 + - + -
1310A THR* 3.2 17.4 - - + +
1368A HIS 4.1 2.9 - - - +
1370A PRO* 3.6 23.0 - - + +
1373A ARG* 2.8 41.4 + - - -
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Residues in contact with ALA1300 (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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1296A MET* 3.8 17.1 - - + +
1297A PRO* 3.0 27.4 + - + +
1299A GLU* 1.3 80.5 - - - +
1301A PHE* 1.3 64.2 + - - +
1304A GLY* 3.0 20.5 + - - -
1305A ILE 3.7 13.0 - - - +
1306A PHE* 3.7 31.4 - - + -
1310A THR* 4.7 0.2 - - + -
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Residues in contact with PHE1301 (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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1291A LEU* 6.3 0.7 - - + -
1293A VAL* 3.2 55.0 - - + -
1296A MET* 3.4 39.3 - - + -
1297A PRO 3.5 13.0 + - - -
1298A PRO* 3.2 13.2 + - + +
1300A ALA* 1.3 81.1 - - - +
1302A MET* 1.3 69.5 + - + +
1304A GLY* 4.0 1.4 + - - -
1338A VAL* 5.5 1.8 - - + -
1339A LEU* 4.0 35.4 - - + -
1342A VAL* 4.4 13.7 - - + -
1343A THR* 4.0 12.6 - - + -
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Residues in contact with MET1302 (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 PRO* 3.0 30.6 + - - +
1299A GLU* 4.6 3.1 - - - +
1301A PHE* 1.3 88.4 - - + +
1303A GLU* 1.3 75.5 + - + +
1343A THR* 4.5 15.9 - - + -
1368A HIS* 5.4 6.5 - - - -
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Residues in contact with GLU1303 (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 GLU* 3.2 11.2 + - + +
1302A MET* 1.3 90.6 - - + +
1304A GLY* 1.3 65.1 + - - +
1305A ILE* 3.4 31.4 + - + +
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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