Contacts of the helix formed by residues 741 - 749 (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 ILE 741 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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686B GLY 3.6 7.2 - - - +
687B LEU* 3.4 47.3 - - + +
734B PRO* 5.4 2.7 - - + -
737B LYS* 4.1 15.3 - - + -
738B THR* 2.5 48.4 + - - +
740B THR* 1.3 76.0 + - - +
742B GLU* 1.3 68.0 + - - +
743B LEU 2.8 1.9 + - - -
744B ILE* 2.8 25.5 + - + +
745B ASP 3.3 4.3 + - - -
746B TYR* 3.4 29.2 + - + -
747B ASP* 4.1 13.5 - - + +
915B ARG* 4.1 6.7 - - - +
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Residues in contact with GLU 742 (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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45B TRP* 6.4 0.2 - - + -
737B LYS* 3.0 29.4 + - - +
738B THR 3.3 7.5 + - - +
739B LYS* 4.3 3.8 + - - +
740B THR 3.4 0.4 - - - -
741B ILE* 1.3 80.2 - - + +
743B LEU* 1.3 71.4 + - + +
745B ASP* 3.4 20.8 + - - +
747B ASP* 2.8 34.4 - - - +
748B LYS* 5.7 3.5 - - - -
975B TYR* 5.7 3.6 - - + -
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Residues in contact with LEU 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 4.1 22.4 - - + +
48B LEU* 3.4 31.9 - - + +
49B PRO* 3.6 31.4 - - + -
52B LEU* 4.0 29.8 - - + +
57B LEU* 4.9 1.2 - - - +
516B LEU* 5.9 2.7 - - + -
739B LYS* 3.2 20.9 - - - +
740B THR* 3.5 8.5 + - - +
741B ILE 3.0 1.6 - - - -
742B GLU* 1.3 90.8 - - + +
744B ILE* 1.3 62.6 + - + +
745B ASP* 3.3 4.1 - - - +
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Residues in contact with ILE 744 (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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52B LEU* 5.9 0.4 - - + -
57B LEU* 3.6 28.3 - - + -
463B TYR* 2.9 31.8 + - + -
464B ILE* 5.6 7.0 - - + -
467B LEU* 4.5 19.5 - - + -
516B LEU* 5.6 7.0 - - + -
683B ALA* 4.1 28.5 - - + +
686B GLY 6.6 0.2 - - - -
687B LEU* 4.9 7.2 - - + +
740B THR 3.6 13.2 + - - +
741B ILE* 2.8 18.7 + - + +
743B LEU* 1.3 79.0 - - + +
745B ASP* 1.3 62.2 + - - +
746B TYR* 3.1 24.5 - - + -
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Residues in contact with ASP 745 (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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179B LEU* 3.5 32.0 - - + +
463B TYR* 4.4 10.5 + - + +
741B ILE 3.3 2.8 + - - -
742B GLU* 3.4 16.4 + - - +
743B LEU* 3.3 4.3 - - - -
744B ILE* 1.3 79.1 - - - +
746B TYR* 1.3 63.6 + - - +
747B ASP* 3.1 8.5 - - - +
748B LYS* 3.0 35.0 + - + +
749B LEU* 3.7 5.0 + - - +
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Residues in contact with TYR 746 (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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463B TYR* 4.4 13.0 - + + -
464B ILE* 3.2 42.5 - - + +
687B LEU* 3.7 21.4 - - + +
734B PRO* 3.7 27.1 - - + -
741B ILE* 3.4 34.2 + - + -
744B ILE* 3.1 21.7 - - + -
745B ASP* 1.3 77.2 - - - +
747B ASP* 1.3 60.9 + - - +
748B LYS 3.2 0.4 - - - -
749B LEU 3.5 19.4 - - - -
750B PRO* 3.5 3.0 - - + +
751B ALA 3.7 20.2 + - - -
915B ARG* 5.2 3.9 + - - -
1023B TYR* 3.6 20.4 - - - -
1025B GLN* 4.2 7.6 + - - -
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Residues in contact with ASP 747 (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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733B GLN* 3.3 35.5 + - + +
734B PRO* 5.2 3.8 - - + -
737B LYS* 4.2 15.3 + - + -
741B ILE* 4.1 6.0 - - + +
742B GLU* 2.8 36.1 - - - +
745B ASP* 4.0 6.6 - - - +
746B TYR* 1.3 79.1 - - - +
748B LYS* 1.3 82.0 + - - +
749B LEU 3.3 0.7 - - - -
750B PRO* 3.6 10.6 - - - +
54J VAL* 3.3 21.7 - - - +
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Residues in contact with LYS 748 (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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179B LEU* 4.4 13.0 - - + +
715B TYR* 3.8 27.1 + - - +
742B GLU* 5.7 3.8 - - - -
745B ASP* 3.0 26.4 + - + +
747B ASP* 1.3 93.8 + - - +
749B LEU* 1.3 71.7 + - - +
750B PRO* 3.6 4.9 - - - +
54J VAL* 4.9 7.8 - - + +
56J LEU* 4.4 9.0 - - - +
59J LYS* 5.8 6.5 - - - +
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Residues in contact with LEU 749 (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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179B LEU* 4.0 23.3 - - + -
463B TYR* 3.4 49.9 + - + +
464B ILE* 5.6 0.3 - - - +
712B ALA* 4.0 23.8 + - + +
713B ILE 3.1 27.4 - - - +
714B ALA* 4.3 8.1 - - + -
715B TYR* 3.9 21.1 - - + +
745B ASP 3.7 2.9 + - - +
746B TYR* 3.5 11.5 + - - +
748B LYS* 1.3 88.1 - - - +
750B PRO* 1.3 67.8 - - - +
751B ALA* 3.5 4.5 + - - +
56J LEU* 4.6 3.8 - - + -
60J PHE* 5.8 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
------------------------------------------------------------
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