Contacts of the helix formed by residues 1299 - 1304 (chain A) in PDB entry 6J8J
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 ARG1299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202A ILE* 3.9 24.2 - - + +
1205A SER* 5.4 0.2 + - - -
1237A PHE* 3.6 45.1 - - - +
1261A LEU* 5.6 1.3 - - - -
1262A ASP* 4.0 29.1 + - - +
1265A ILE* 3.0 49.4 - - + +
1266A VAL* 3.7 19.4 - - - +
1269A SER* 4.6 9.1 + - - -
1296A ARG* 3.0 48.1 + - - +
1298A LEU* 1.3 76.6 - - - +
1300A ALA* 1.3 63.1 + - - +
1301A LEU 2.9 1.8 + - - -
1302A SER* 3.3 16.5 + - - -
1303A ARG* 4.0 10.7 + - - +
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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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1202A ILE* 3.7 23.0 - - + +
1203A LEU* 5.6 3.6 - - + -
1206A SER* 5.5 1.1 - - - +
1297A PRO* 3.0 18.3 + - + +
1298A LEU 2.9 0.2 - - - -
1299A ARG* 1.3 80.6 - - - +
1301A LEU* 1.3 60.3 + - - +
1302A SER 3.3 0.2 - - - -
1303A ARG* 3.4 13.8 + - - +
1304A PHE* 3.4 35.0 - - + -
1307A MET* 4.1 0.4 - - - +
1653A LEU* 3.9 14.4 - - + -
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Residues in contact with LEU1301 (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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1258A TRP* 4.6 17.5 - - + -
1261A LEU* 5.1 5.6 - - + -
1297A PRO 4.3 0.2 + - - -
1298A LEU* 2.9 48.1 + - + +
1300A ALA* 1.3 79.7 - - - +
1302A SER* 1.3 61.0 + - - +
1304A PHE 3.8 13.2 + - - +
1307A MET* 4.1 12.3 - - + +
1308A ARG* 3.8 16.4 + - - +
1311A VAL* 3.3 34.5 - - + -
1650A LEU* 3.8 15.0 - - + -
1653A LEU* 3.8 18.5 - - + +
1654A VAL* 6.5 0.2 - - + -
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Residues in contact with SER1302 (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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1258A TRP* 4.3 35.3 - - - +
1262A ASP* 5.4 7.0 - - - -
1299A ARG 3.3 10.0 + - - -
1301A LEU* 1.3 79.0 - - - +
1303A ARG* 1.3 66.3 + - - +
1308A ARG* 2.5 38.6 + - - +
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Residues in contact with ARG1303 (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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1194A PHE* 5.9 0.6 - - - -
1195A GLU* 3.0 38.4 + - - -
1198A ILE* 3.2 20.6 - - - +
1199A VAL* 3.9 25.2 - - + +
1202A ILE* 3.2 30.6 - - + +
1237A PHE* 5.7 1.2 - - - -
1240A GLU* 3.2 26.1 + - - -
1244A LYS* 4.8 4.8 - - - +
1262A ASP* 3.9 18.6 + - - -
1299A ARG* 4.0 11.7 + - - +
1300A ALA* 3.7 8.1 - - - +
1301A LEU 3.4 1.0 - - - -
1302A SER* 1.3 82.7 + - - +
1304A PHE* 1.3 68.7 + - + +
1305A GLU* 3.7 6.9 + - - +
1308A ARG* 4.5 1.4 + - - -
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Residues in contact with PHE1304 (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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1199A VAL* 4.1 22.4 - - + -
1202A ILE* 6.2 0.7 - - + -
1203A LEU* 4.0 28.9 - - + -
1300A ALA* 3.4 31.0 + - + -
1301A LEU 3.8 0.9 + - - +
1302A SER 3.5 0.4 - - - -
1303A ARG* 1.3 80.4 - - + +
1305A GLU* 1.3 72.2 + - - +
1306A GLY 4.5 1.8 - - - +
1307A MET* 2.9 42.0 - - + +
1308A ARG* 3.0 26.1 + - - +
1649A LEU* 4.8 10.3 - - + -
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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