Contacts of the helix formed by residues 1308 - 1313 (chain D) in PDB entry 6RI7
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 GLY1308 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1145D PHE 3.6 6.3 - - - -
1146D GLU* 3.3 30.8 + - - -
1147D ALA* 4.5 2.1 - - - +
1218D HIS* 5.8 1.0 + - - -
1306D LEU* 4.2 2.6 - - - +
1307D LEU* 1.3 74.0 - - - +
1309D ILE* 1.3 61.0 + - - -
1310D THR* 3.2 3.8 - - - -
1311D LYS* 2.8 29.5 + - - +
1312D ALA* 2.9 11.9 + - - -
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Residues in contact with ILE1309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796D LEU* 5.1 2.0 - - + -
799D ARG* 3.6 42.0 - - + +
800D LEU* 4.1 19.3 - - + -
803D VAL* 4.1 36.0 - - + +
1142D ALA 5.9 0.9 - - - +
1145D PHE* 3.2 34.2 + - + +
1146D GLU* 4.3 8.5 - - - +
1256D ILE* 5.0 1.8 - - + -
1260D MET* 4.2 15.5 - - + -
1307D LEU 3.8 0.6 + - - -
1308D GLY* 1.3 70.8 - - - -
1310D THR* 1.3 64.6 + - - +
1311D LYS 2.6 11.6 + - - -
1312D ALA* 4.4 2.7 - - - +
1313D SER* 2.9 26.2 + - - -
1325D PHE* 5.7 0.7 - - - -
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Residues in contact with THR1310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795D TYR* 4.9 0.5 + - - -
799D ARG* 4.9 5.6 - - - -
1146D GLU* 3.1 34.8 - - - +
1308D GLY 4.7 0.4 - - - +
1309D ILE* 1.3 82.6 - - - +
1311D LYS* 1.3 70.1 + - + +
1313D SER* 3.0 14.8 + - - -
1314D LEU* 3.5 15.8 - - - +
1325D PHE* 4.9 1.8 - - - -
1326D GLN* 2.8 35.5 + - - +
27N A 5.6 5.2 - - - -
28N A 5.9 0.7 - - - +
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Residues in contact with LYS1311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146D GLU* 5.5 0.4 - - - +
1307D LEU* 3.9 23.1 - - + -
1308D GLY* 2.8 14.8 + - - +
1309D ILE 2.6 0.4 + - - -
1310D THR* 1.3 95.6 - - + +
1312D ALA* 1.3 57.2 + - - +
1313D SER 3.0 1.6 - - - -
1314D LEU* 2.3 44.7 + - + +
1315D ALA* 3.0 10.2 + - - +
1330D ARG* 6.4 0.4 - - - +
28N A 4.2 32.6 + - - +
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Residues in contact with ALA1312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803D VAL* 4.4 13.5 - - + -
1259D GLN 4.1 20.6 - - - +
1260D MET* 5.1 0.4 - - - +
1262D ARG* 3.4 15.3 + - + +
1263D LYS* 5.8 4.7 - - + -
1307D LEU* 4.0 23.4 - - + +
1308D GLY 2.9 13.6 + - - +
1309D ILE* 4.1 3.1 - - - +
1311D LYS* 1.3 74.8 - - - +
1313D SER* 1.3 52.2 + - - +
1315D ALA* 4.2 2.6 - - - +
1316D THR* 2.6 32.6 + - - -
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Residues in contact with SER1313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802D ASP 4.1 17.0 - - - -
803D VAL* 4.9 3.1 - - - +
1309D ILE 2.9 14.2 + - - -
1310D THR 3.0 22.7 + - - -
1312D ALA* 1.3 73.9 - - - +
1314D LEU* 1.3 76.5 + - - +
1316D THR* 2.6 23.3 + - - -
1321D SER* 6.0 0.5 - - - -
1322D ALA* 4.1 10.4 + - - +
1325D PHE* 3.5 33.2 - - - -
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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