Contacts of the helix formed by residues 1063 - 1074 (chain B) 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 GLY1063 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A GLY* 4.5 2.9 - - - -
1061B ARG* 3.8 8.6 + - - -
1062B LEU* 1.3 75.4 - - - +
1064B GLU* 1.3 67.9 + - - -
1065B MET* 3.0 4.5 - - - -
1066B GLU* 2.9 11.5 + - - +
1067B ARG* 2.8 24.0 + - - +
23Y G 4.7 4.5 - - - -
24Y T 3.5 23.0 + - - -
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Residues in contact with GLU1064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A ARG* 3.0 34.2 - - + +
369A SER* 4.4 21.3 - - - +
370A GLY* 4.3 7.7 - - - -
887A ARG* 2.5 48.5 + - + +
890A MET* 3.9 22.8 - - + +
891A LYS* 3.8 23.9 + - + +
1388A SER* 4.2 4.8 + - - +
1061B ARG* 5.1 3.0 - - - +
1063B GLY* 1.3 72.1 - - - +
1065B MET* 1.3 62.3 + - - +
1067B ARG* 4.0 12.8 + - - +
1068B ASP 4.1 5.2 + - - -
23Y G 5.2 4.0 + - - +
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Residues in contact with MET1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A PRO* 5.3 4.0 - - + -
479A SER* 3.3 39.1 + - - +
480A LEU* 4.1 15.5 - - + +
883A GLY* 4.5 23.1 - - - +
886A SER* 4.3 21.5 - - - +
887A ARG* 4.8 11.8 - - + +
890A MET* 5.3 2.8 - - - +
1095A GLN* 5.3 5.9 + - - +
1063B GLY* 3.0 2.1 - - - -
1064B GLU* 1.3 81.9 - - - +
1066B GLU* 1.3 62.9 + - + +
1068B ASP* 3.8 13.0 - - - +
1069B CYS 4.6 0.5 + - - -
22Y T 5.9 4.7 - - + +
23Y G 4.7 25.8 + - + +
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Residues in contact with GLU1066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A ASN* 4.0 20.2 - - - +
477A GLN 5.7 0.7 - - - +
479A SER* 3.1 26.0 - - - +
485A ILE* 3.0 31.5 - - + +
1061B ARG 5.6 0.7 - - - +
1062B LEU* 3.1 36.9 - - + +
1063B GLY* 2.9 14.5 + - - +
1065B MET* 1.3 77.2 - - + +
1067B ARG* 1.3 71.4 + - - +
1068B ASP 3.0 2.5 - - - -
1069B CYS* 2.7 33.9 + - + +
1070B VAL* 4.4 6.9 - - - +
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Residues in contact with ARG1067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A SER* 3.4 25.6 + - - +
890A MET* 4.1 16.2 - - - +
891A LYS* 4.2 10.5 - - - +
894A GLU* 2.9 35.1 + - - -
1411A VAL* 4.6 1.2 - - - +
1412A SER* 4.5 0.2 - - - -
1415A ILE* 3.5 31.4 - - - +
1062B LEU* 5.3 5.2 - - + +
1063B GLY 2.8 17.8 + - - +
1064B GLU* 4.3 6.6 + - - +
1066B GLU* 1.3 84.1 + - - +
1068B ASP* 1.3 65.2 + - - +
1069B CYS 3.0 0.9 + - - -
1070B VAL* 3.1 26.8 - - + +
1071B ILE* 3.4 24.9 + - - +
1079B LEU* 4.3 11.9 - - + -
1083B LEU* 3.7 27.8 - - + -
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Residues in contact with ASP1068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890A MET* 3.1 42.0 - - - +
894A GLU* 4.4 8.1 - - - +
1091A ALA* 4.5 12.7 - - - +
1094A ALA* 5.6 0.7 - - - +
1095A GLN* 2.2 44.7 + - - +
1064B GLU 4.1 2.6 + - - -
1065B MET 3.8 13.1 + - - +
1066B GLU 2.9 0.4 + - - -
1067B ARG* 1.3 81.4 - - - +
1069B CYS* 1.3 64.8 + - - +
1071B ILE* 2.9 24.6 + - - +
1072B ALA* 2.9 10.4 + - - +
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Residues in contact with CYS1069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A SER* 5.0 3.8 - - - +
481A HIS 3.7 11.7 - - - +
482A ARG* 3.0 35.9 - - - +
484A SER* 4.0 1.6 - - - -
485A ILE* 3.9 32.3 - - + -
1095A GLN* 5.3 1.3 - - - +
1065B MET 4.6 0.6 + - - +
1066B GLU* 2.7 23.9 + - + +
1068B ASP* 1.3 72.9 + - - +
1070B VAL* 1.3 58.4 + - - +
1072B ALA* 2.8 26.5 + - - +
1073B TYR* 3.2 22.4 + - - -
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Residues in contact with VAL1070 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A LEU* 6.0 0.4 - - + -
485A ILE* 4.2 15.5 - - + -
535A MET* 3.6 26.9 - - + -
1062B LEU* 6.4 2.9 - - + -
1066B GLU* 4.4 9.2 - - - +
1067B ARG* 3.1 20.3 + - + +
1069B CYS* 1.3 75.3 - - - +
1071B ILE* 1.3 63.0 + - - +
1073B TYR* 3.5 9.9 + - - +
1074B GLY 3.3 2.9 + - - -
1075B ALA 3.2 28.3 + - - +
1078B LEU* 4.3 11.4 - - + -
1079B LEU* 3.6 31.0 - - + -
1083B LEU* 6.2 2.0 - - + -
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Residues in contact with ILE1071 (chain B).
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* 4.5 14.8 - - + +
1088A ALA* 4.6 4.7 - - - +
1091A ALA* 4.1 16.3 - - + +
1411A VAL* 3.5 31.4 - - + -
1421A MET* 3.5 11.9 - - + -
1423A ILE* 4.6 13.4 - - + +
1067B ARG* 3.6 28.7 - - - +
1068B ASP* 2.9 19.7 + - - +
1070B VAL* 1.3 78.0 - - - +
1072B ALA* 1.3 52.8 + - - +
1074B GLY* 2.6 28.4 + - - +
1079B LEU* 3.4 26.9 - - + -
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Residues in contact with ALA1072 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A ARG* 3.9 36.0 + - + -
1087A THR* 4.9 5.4 - - - +
1088A ALA 4.6 5.5 + - - +
1091A ALA* 3.7 23.0 - - + +
1092A ILE* 4.1 21.1 - - + +
1095A GLN* 4.7 5.6 - - + -
1068B ASP 2.9 8.8 + - - +
1069B CYS* 2.8 17.4 + - - +
1071B ILE* 1.3 72.8 - - - +
1073B TYR* 1.3 61.8 + - - +
1074B GLY* 3.2 0.7 + - - -
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Residues in contact with TYR1073 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A ARG* 2.4 52.8 + - + +
483A LEU* 3.5 13.2 - - - +
485A ILE 2.9 20.0 + - - -
486A LEU* 4.0 1.0 - - - +
534A LEU* 4.0 12.2 - - + +
535A MET* 3.5 49.8 - - + -
540A ASN* 3.0 38.1 - - - -
1069B CYS* 3.2 36.0 + - - -
1070B VAL 3.8 1.6 - - - +
1071B ILE 3.2 0.8 - - - -
1072B ALA* 1.3 76.8 - - - +
1074B GLY* 1.3 61.0 + - - +
1075B ALA* 4.3 2.7 - - + +
87F LYS* 5.1 0.9 + - - -
88F TYR* 3.4 23.2 + - - -
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Residues in contact with GLY1074 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A GLU* 3.7 0.7 - - - +
534A LEU* 4.1 2.2 - - - +
1088A ALA 5.7 3.1 - - - -
1421A MET* 5.5 2.5 - - - -
1423A ILE* 5.0 4.0 - - - -
1424A GLY* 4.0 17.0 - - - -
1425A THR* 3.1 31.3 + - - -
1070B VAL 3.3 0.4 + - - -
1071B ILE* 2.6 24.7 + - - -
1072B ALA 3.0 0.8 - - - -
1073B TYR* 1.3 74.8 - - - +
1075B ALA* 1.3 59.9 + - - +
1076B SER 3.8 0.4 - - - -
88F TYR* 4.6 5.3 - - - -
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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