Contacts of the helix formed by residues 789 - 794 (chain A) 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 ASN 789 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710A PHE* 5.6 0.9 - - - -
715A ASN 5.4 0.4 + - - -
716A ASP* 3.0 34.7 + - + +
785A LEU* 3.2 35.4 - - - +
786A ASP* 2.9 26.2 + - + +
787A ASN 4.3 2.2 - - - +
788A TRP* 1.3 76.9 - - - +
790A ALA* 1.3 53.5 + - - +
791A PRO 3.6 0.7 - - - -
792A LEU* 2.8 40.7 + - - +
793A ILE* 3.1 10.4 + - - +
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Residues in contact with ALA 790 (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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710A PHE* 3.5 30.7 - - + -
711A SER 3.7 15.4 + - - +
712A ILE* 3.8 9.0 - - + -
716A ASP* 2.3 26.8 + - - +
789A ASN* 1.3 63.3 - - - +
791A PRO* 1.3 68.6 - - + +
792A LEU 2.8 6.2 + - - -
793A ILE 3.3 1.5 + - - +
794A MET* 2.9 41.2 + - + +
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Residues in contact with PRO 791 (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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712A ILE* 4.3 7.9 - - + -
716A ASP* 3.0 36.8 - - - +
717A VAL* 4.2 20.6 - - + -
785A LEU* 5.4 2.7 - - + -
790A ALA* 1.3 79.8 - - + +
792A LEU* 1.3 56.6 + - - +
794A MET* 4.6 7.0 - - + -
795A ALA* 3.3 27.8 - - + +
796A THR* 3.7 3.1 + - - -
806A VAL* 3.6 37.3 - - + +
809A MET* 4.8 5.6 - - - -
950B PRO* 4.7 15.0 - - + -
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Residues in contact with LEU 792 (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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562A TYR* 5.9 1.3 - - - +
782A ILE* 4.3 17.5 - - + +
785A LEU* 4.5 12.8 - - + +
786A ASP 3.7 21.5 - - - +
787A ASN* 5.0 5.6 - - - +
788A TRP 5.3 0.7 - - - +
789A ASN* 2.8 19.4 + - - +
791A PRO* 1.3 74.5 - - - +
793A ILE* 1.3 92.1 + - + +
794A MET 2.8 3.2 + - - -
795A ALA 3.0 0.3 + - - -
796A THR* 2.6 55.6 + - + +
797A CYS* 5.3 3.1 - - - -
19H ARG* 3.2 35.0 - - - +
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Residues in contact with ILE 793 (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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559A THR* 4.5 11.7 + - - +
562A TYR* 3.5 36.6 - - + +
563A LEU* 4.1 16.2 - - + -
566A HIS* 6.1 4.0 - - + -
665A ASP* 4.4 2.1 - - - +
710A PHE* 4.5 18.8 - - + -
787A ASN* 5.4 1.6 - - - +
788A TRP* 3.6 47.8 - - + +
789A ASN 3.1 11.3 + - - +
790A ALA 4.5 1.1 - - - +
792A LEU* 1.3 91.3 - - + +
794A MET* 1.3 62.8 + - - +
796A THR* 5.0 0.4 - - - -
797A CYS* 3.7 10.3 - - - +
798A GLY* 3.6 9.7 + - - -
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Residues in contact with MET 794 (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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559A THR* 4.5 9.9 - - - +
710A PHE* 4.0 20.4 - - + -
712A ILE* 4.2 8.3 - - + -
790A ALA* 2.9 37.3 + - + +
791A PRO* 4.2 0.4 - - + -
792A LEU 2.8 2.8 + - - -
793A ILE* 1.3 71.5 - - - +
795A ALA* 1.3 64.6 + - + +
797A CYS 3.0 0.5 + - - -
798A GLY 2.6 30.9 + - - +
799A SER* 3.4 12.7 + - - +
800A LYS* 4.1 12.1 - - - +
946B PRO 5.2 0.2 - - - -
947B HIS* 3.1 44.6 - - + +
950B PRO* 3.5 32.5 - - + -
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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