Contacts of the helix formed by residues 1410 - 1418 (chain A) in PDB entry 6CNC
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 GLY1410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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895A ASP* 3.4 15.3 - - - -
907A SER* 3.1 15.0 + - - -
1382A SER* 4.7 3.8 + - - -
1385A GLN* 5.8 3.6 - - - -
1409A GLU* 1.3 84.8 - - - +
1411A VAL* 1.3 61.0 + - - -
1412A SER 3.8 0.4 - - - -
1413A GLU* 3.9 10.7 - - - +
1414A CYS* 3.1 24.3 + - - -
1422A SER* 5.8 2.9 - - - -
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Residues in contact with VAL1411 (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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894A GLU* 3.6 38.4 - - + +
895A ASP* 4.1 13.1 + - + +
1385A GLN* 5.7 0.2 + - - -
1410A GLY* 1.3 69.1 - - - -
1412A SER* 1.3 67.3 + - - +
1413A GLU 2.8 10.0 + - - -
1414A CYS* 2.8 16.6 + - - +
1415A ILE* 2.9 20.4 + - + +
1421A MET* 3.9 28.3 - - + -
1423A ILE* 4.9 7.6 - - + -
1071B ILE* 3.5 35.0 - - + -
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Residues in contact with SER1412 (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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891A LYS* 3.6 17.2 + - - -
894A GLU* 3.2 28.5 + - - -
1385A GLN* 2.8 37.7 + - - +
1388A SER* 5.1 2.8 + - - -
1411A VAL* 1.3 79.7 - - - +
1413A GLU* 1.3 57.9 + - - +
1415A ILE* 3.6 17.5 - - - +
1416A ILE* 3.4 23.7 - - - +
1067B ARG* 4.5 2.0 - - - -
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Residues in contact with GLU1413 (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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16A LEU* 4.8 1.6 - - - +
1382A SER* 3.9 16.0 - - - +
1384A LEU* 2.9 50.9 + - - +
1385A GLN* 3.6 10.9 + - + +
1406A ASP* 3.6 15.3 - - - +
1408A VAL* 3.4 32.9 - - + +
1409A GLU 3.8 9.0 - - - +
1410A GLY* 3.5 19.2 - - - +
1411A VAL 2.8 1.0 + - - -
1412A SER* 1.3 79.0 + - - +
1414A CYS* 1.3 65.6 + - - +
1416A ILE* 3.0 23.4 + - - +
1417A LEU* 3.7 4.7 + - - +
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Residues in contact with CYS1414 (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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1408A VAL* 4.0 11.7 - - - -
1409A GLU* 3.6 13.0 - - - -
1410A GLY 3.1 21.6 + - - +
1411A VAL* 2.8 10.1 + - - +
1413A GLU* 1.3 77.5 - - - +
1415A ILE* 1.3 50.4 + - + +
1416A ILE 3.0 0.3 + - - -
1417A LEU* 3.2 3.0 + - - +
1418A GLY* 2.5 35.3 + - - -
1419A GLN* 3.3 36.5 + - + +
1420A THR 3.4 24.5 - - - +
1421A MET* 4.9 5.6 - - + -
1422A SER* 5.2 2.9 - - - -
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Residues in contact with ILE1415 (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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368A LEU* 5.1 4.8 - - - +
369A SER* 4.0 16.2 - - - +
371A LYS* 4.7 5.2 + - - -
1411A VAL* 2.9 23.7 + - + +
1412A SER* 3.6 24.0 - - - +
1414A CYS* 1.3 76.5 - - + +
1416A ILE* 1.3 66.8 + - + +
1418A GLY* 3.4 11.3 + - - +
1419A GLN 5.0 2.2 - - - +
1421A MET* 4.7 1.6 - - + -
1067B ARG* 3.5 43.1 - - - +
1079B LEU* 3.5 35.4 - - + -
1083B LEU* 4.9 13.5 - - + +
1122B PRO* 4.5 3.8 - - - +
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Residues in contact with ILE1416 (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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364A PHE* 4.6 11.2 - - + -
368A LEU* 3.5 40.5 - - + +
369A SER* 5.6 3.6 - - - +
371A LYS* 4.6 1.6 + - - +
1384A LEU* 4.0 37.5 - - + -
1388A SER* 4.5 17.3 - - - +
1412A SER 3.4 21.3 - - - +
1413A GLU 3.0 7.4 + - - +
1414A CYS 2.9 1.6 - - - -
1415A ILE* 1.3 81.6 - - + +
1417A LEU* 1.3 66.8 + - + +
1418A GLY 2.9 4.0 + - - -
1122B PRO* 3.4 14.2 - - - +
1125B ALA* 3.4 17.4 - - + +
1128B LEU* 5.5 6.3 - - + -
1129B PHE* 6.2 1.8 - - + -
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Residues in contact with LEU1417 (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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13A ILE* 3.7 46.9 - - + +
16A LEU* 3.7 17.0 - - + -
1384A LEU* 5.2 4.0 - - + -
1408A VAL* 3.8 20.9 - - + -
1413A GLU* 3.7 5.3 + - - +
1414A CYS 3.2 7.0 + - - +
1416A ILE* 1.3 82.0 - - + +
1418A GLY* 1.3 63.2 + - - +
1419A GLN* 3.1 8.6 + - + +
1120B THR 4.9 1.4 - - - +
1121B ILE* 3.9 18.4 - - + +
1122B PRO* 3.2 14.0 - - - +
1125B ALA* 4.6 4.0 - - + -
1129B PHE* 3.6 34.5 - - + -
1141B LEU* 4.7 4.0 - - + -
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Residues in contact with GLY1418 (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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1414A CYS 2.5 15.7 + - - -
1415A ILE* 3.7 8.5 - - - -
1416A ILE 2.9 4.2 - - - -
1417A LEU* 1.3 73.2 - - - +
1419A GLN* 1.3 63.4 + - - +
1080B LEU* 3.3 18.7 - - - +
1083B LEU 5.9 0.4 - - - -
1084B MET* 4.2 16.7 - - - +
1122B PRO* 3.6 19.5 - - - -
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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