Contacts of the helix formed by residues 1076 - 1083 (chain B) in PDB entry 6CNB
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 SER1076 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1420A THR* 5.1 3.1 - - - -
1421A MET* 3.7 40.8 - - - -
1423A ILE 4.9 0.2 - - - -
1425A THR* 3.9 6.4 - - - +
1426A GLY* 3.7 23.1 + - - -
1074B GLY 3.2 6.4 + - - -
1075B ALA* 1.3 70.3 - - - +
1077B GLN* 1.3 93.6 + - - +
1078B LEU 3.1 2.0 - - - -
1079B LEU* 3.0 16.5 + - - +
1080B LEU* 3.1 15.5 + - - +
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Residues in contact with GLN1077 (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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524A THR* 5.1 2.6 - - - +
526A GLU* 3.3 46.9 - - + +
527A ALA* 4.1 5.1 - - + +
530A GLU* 4.7 10.9 - - + +
1420A THR* 4.1 11.5 - - - +
1425A THR* 4.6 8.1 - - + -
1075B ALA* 3.6 0.6 - - - +
1076B SER* 1.3 94.3 + - - +
1078B LEU* 1.3 56.5 + - - +
1080B LEU* 3.9 12.0 - - - +
1081B GLU* 2.9 28.9 + - - +
92F ARG* 3.3 31.3 - - + +
61G PRO* 3.6 19.2 - - - +
62G GLY* 5.4 1.4 - - - -
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Residues in contact with LEU1078 (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* 3.6 29.4 - - + -
522A PRO* 4.8 5.8 - - + -
527A ALA* 4.5 18.6 - - + +
530A GLU* 4.4 9.0 - - + +
531A ALA* 5.3 4.5 - - + -
535A MET* 3.5 37.2 - - + -
1070B VAL* 3.7 15.0 - - + -
1075B ALA* 3.7 18.1 - - + +
1076B SER 3.1 0.8 - - - -
1077B GLN* 1.3 76.8 - - - +
1079B LEU* 1.3 60.5 + - + +
1081B GLU* 3.4 14.7 + - - +
1082B ARG* 2.9 35.3 + - + +
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Residues in contact with LEU1079 (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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1415A ILE* 3.8 16.2 - - + -
1421A MET* 3.5 17.0 - - + -
1062B LEU* 6.2 0.2 - - + -
1067B ARG* 4.2 13.2 - - + +
1070B VAL* 3.6 25.8 - - + -
1071B ILE* 3.5 32.8 - - + -
1075B ALA 4.1 5.3 + - - +
1076B SER 3.0 7.8 + - - +
1078B LEU* 1.3 75.7 - - - +
1080B LEU* 1.3 64.7 + - + +
1082B ARG* 2.4 25.8 + - + -
1083B LEU* 2.6 43.7 + - + -
1084B MET 3.7 0.9 + - - -
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Residues in contact with LEU1080 (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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1414A CYS 5.6 0.7 - - - +
1415A ILE* 5.8 4.9 - - + -
1418A GLY* 3.5 21.3 - - - +
1419A GLN* 3.2 38.8 - - - +
1420A THR* 3.6 26.0 - - + +
1421A MET* 5.3 4.5 - - + +
1076B SER* 3.1 15.9 + - - +
1077B GLN* 4.1 15.0 - - - +
1079B LEU* 1.3 83.7 - - + +
1081B GLU* 1.3 58.0 + - - +
1084B MET* 2.9 13.4 - - + +
1085B ILE* 2.9 37.2 + - + +
62G GLY* 6.5 0.9 - - - -
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Residues in contact with GLU1081 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A PRO* 4.1 1.3 - - - -
523A GLN* 3.5 26.1 + - + +
524A THR* 4.0 15.0 - - + +
527A ALA* 3.8 16.6 - - + -
1077B GLN 2.9 19.4 + - - +
1078B LEU* 3.4 8.1 - - - +
1080B LEU* 1.3 75.7 - - - +
1082B ARG* 1.3 106.8 + - - +
1085B ILE* 3.7 11.7 - - + +
1086B SER* 2.3 54.5 + - - +
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Residues in contact with ARG1082 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A VAL* 3.4 25.1 - - - +
374A ASP 3.3 24.5 + - - -
375A PHE* 4.5 3.4 + - - +
473A LEU* 5.0 3.0 - - - +
520A HIS* 4.5 15.7 + - - +
521A VAL 2.6 29.6 + - - -
522A PRO* 3.2 8.7 - - - +
1062B LEU* 3.4 29.2 - - + -
1078B LEU* 2.9 25.5 + - + +
1079B LEU* 2.4 23.3 + - + +
1081B GLU* 1.3 109.3 + - - +
1083B LEU* 1.3 63.7 + - + +
1084B MET 3.1 6.2 + - - -
1086B SER* 4.0 6.5 + - - -
1087B SER* 3.2 22.7 + - - -
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Residues in contact with LEU1083 (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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368A LEU 4.5 7.9 - - - +
369A SER* 3.4 30.1 - - - +
371A LYS* 3.2 44.8 - - + +
373A VAL* 5.3 0.9 - - + -
1415A ILE* 4.9 19.6 - - + +
1062B LEU* 3.8 17.7 - - + -
1067B ARG* 3.7 20.0 - - + -
1079B LEU* 2.6 33.7 + - + +
1082B ARG* 1.3 92.9 - - + +
1084B MET* 1.3 56.9 + - - +
1087B SER* 4.7 1.8 - - - -
1088B ASP* 4.0 1.4 - - - +
1122B PRO* 4.1 8.5 - - - +
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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