Contacts of the helix formed by residues 1271 - 1276 (chain A) in PDB entry 6Q6Q
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 SER1271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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925A PHE* 5.0 0.3 - - - -
1012A LEU* 3.8 37.4 - - - +
1014A PHE* 3.6 27.5 - - - -
1163A VAL* 3.8 8.9 - - - +
1189A MET* 3.9 11.2 - - - -
1268A LEU* 3.4 27.0 + - - -
1270A GLU* 1.3 73.9 - - - +
1272A GLY* 1.3 60.8 + - - +
1273A VAL 3.0 10.2 + - - -
1274A PHE* 3.3 11.3 + - - +
1275A LEU 3.8 1.4 + - - -
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Residues in contact with GLY1272 (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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1189A MET* 5.1 2.7 - - - +
1204A ILE* 4.5 11.5 - - - +
1207A ALA* 3.6 20.0 - - - +
1208A PHE* 3.3 20.8 - - - -
1268A LEU 4.5 2.0 + - - -
1270A GLU 3.6 0.2 - - - -
1271A SER* 1.3 76.5 - - - +
1273A VAL* 1.3 63.6 + - - +
1274A PHE 3.2 0.4 - - - -
1275A LEU* 3.1 28.0 + - - +
1276A GLY 3.3 4.0 + - - -
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Residues in contact with VAL1273 (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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748A GLN* 5.8 0.2 - - - +
848A ARG* 3.7 24.0 - - - +
921A ARG* 4.0 26.0 - - + +
926A PRO* 3.8 17.9 - - + -
1207A ALA* 3.2 27.6 - - + +
1210A GLN* 4.8 5.8 - - + +
1211A GLY* 3.3 27.2 - - - +
1214A LEU* 4.7 3.4 - - + -
1215A TYR* 3.6 8.0 - - - -
1270A GLU* 3.7 18.2 - - - +
1271A SER 3.0 1.0 + - - -
1272A GLY* 1.3 76.7 - - - +
1274A PHE* 1.3 61.8 + - - +
1276A GLY 3.3 7.8 + - - -
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Residues in contact with PHE1274 (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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896A ASN* 3.5 22.2 - - - -
925A PHE* 3.5 26.9 - + + -
926A PRO* 4.5 7.7 - - + +
929A ALA* 3.4 32.8 - - + -
930A LEU* 4.1 2.7 - - - -
933A GLU* 3.7 17.5 - - + -
1010A VAL* 4.2 7.2 - - + -
1011A PRO 3.1 24.5 - - - -
1012A LEU* 3.6 19.7 - - + -
1215A TYR* 4.1 15.3 - - - -
1270A GLU 4.7 0.6 + - - -
1271A SER 3.3 5.1 + - - +
1272A GLY 3.2 0.2 - - - -
1273A VAL* 1.3 74.7 - - - +
1275A LEU* 1.3 59.2 + - + +
1276A GLY 3.0 5.2 - - - -
1277A CYS* 2.8 49.9 + - + +
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Residues in contact with LEU1275 (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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1010A VAL* 4.3 13.0 - - + +
1012A LEU* 3.6 35.2 - - + -
1166A ALA* 4.3 5.8 - - - +
1167A ALA* 3.7 30.8 - - + +
1187A ILE* 3.9 22.9 - - + -
1189A MET* 3.7 29.8 - - - -
1204A ILE* 5.6 0.4 - - + -
1208A PHE* 3.5 11.2 - - + -
1271A SER 3.8 0.6 + - - +
1272A GLY* 3.1 20.5 + - - +
1274A PHE* 1.3 77.9 - - + +
1276A GLY* 1.3 53.8 + - - +
1277A CYS 3.1 1.2 + - - -
1278A SER* 2.8 30.2 + - - -
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Residues in contact with GLY1276 (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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1208A PHE* 3.5 30.1 - - - -
1212A MET* 3.8 6.4 - - - -
1215A TYR* 3.3 16.5 - - - -
1272A GLY 3.3 8.7 + - - -
1273A VAL 3.3 6.9 + - - -
1274A PHE 3.0 2.2 - - - -
1275A LEU* 1.3 74.9 - - - +
1277A CYS* 1.3 56.0 + - - +
1278A SER 3.2 2.0 - - - -
1279A VAL* 3.1 23.6 - - - +
1280A PHE 4.2 0.2 + - - -
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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