Contacts of the helix formed by residues 777 - 791 (chain N) in PDB entry 6AH0
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 PRO 777 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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776N ASN* 1.3 70.2 - - - +
778N GLY* 1.3 53.6 + - - +
779N LEU 2.7 17.5 + - - -
780N TRP* 2.8 16.8 + - - -
781N LEU 3.7 5.0 + - - -
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Residues in contact with GLY 778 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743N THR* 5.8 6.1 - - - +
776N ASN 3.7 0.4 - - - -
777N PRO* 1.3 74.1 - - - +
779N LEU* 1.3 58.2 + - - +
780N TRP 3.5 0.2 - - - -
781N LEU* 3.8 4.7 + - - -
782N GLU* 3.3 17.0 + - - -
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Residues in contact with LEU 779 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743N THR* 5.8 6.2 - - - +
770N ARG* 6.2 3.6 - - - +
776N ASN 4.3 4.8 + - - -
777N PRO 2.7 7.9 + - - -
778N GLY* 1.3 71.5 - - - +
780N TRP* 1.3 62.1 + - - +
781N LEU 3.2 0.2 - - - -
782N GLU* 3.2 4.0 + - - +
783N SER* 3.1 17.8 + - - -
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Residues in contact with TRP 780 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776N ASN 4.6 3.0 + - - -
777N PRO 2.8 8.6 + - - -
779N LEU* 1.3 76.7 - - - +
781N LEU* 1.3 58.3 + - - +
783N SER* 3.2 3.0 + - - +
784N VAL* 2.9 24.6 + - - -
803N ALA* 6.5 1.3 - - - +
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Residues in contact with LEU 781 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777N PRO 3.7 6.9 + - - -
778N GLY* 3.8 4.4 + - - -
779N LEU 3.2 0.6 - - - -
780N TRP* 1.3 72.1 - - - +
782N GLU* 1.3 56.4 + - - +
784N VAL* 3.1 2.0 + - - +
785N ARG* 2.5 37.5 + - - +
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Residues in contact with GLU 782 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747N LEU* 6.2 4.3 - - - +
778N GLY 3.3 12.2 + - - -
779N LEU* 3.2 8.1 + - - +
781N LEU* 1.3 75.9 - - - +
783N SER* 1.3 56.6 + - - +
785N ARG* 5.1 0.4 - - - +
786N LEU* 2.9 28.1 + - - -
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Residues in contact with SER 783 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779N LEU 3.1 12.1 + - - -
780N TRP* 3.2 4.2 + - - +
782N GLU* 1.3 75.0 - - - +
784N VAL* 1.3 52.8 + - - +
786N LEU 3.6 1.0 - - - -
787N GLU* 2.8 32.1 + - - -
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Residues in contact with VAL 784 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780N TRP 2.9 13.9 + - - -
781N LEU* 3.5 3.1 - - - +
783N SER* 1.3 74.8 - - - +
785N ARG* 1.3 55.3 - - - +
787N GLU* 2.7 23.5 + - - +
788N TYR* 3.0 10.6 + - - -
796N ALA* 5.8 9.4 - - - +
799N LEU* 6.2 5.2 - - - +
800N MET 6.2 0.2 - - - +
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Residues in contact with ARG 785 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781N LEU 2.5 21.0 + - - -
782N GLU* 3.9 0.7 - - - +
784N VAL* 1.3 71.9 - - - +
786N LEU* 1.3 57.0 + - - +
788N TYR* 3.8 1.6 + - - +
789N ARG* 3.8 14.6 + - - -
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Residues in contact with LEU 786 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782N GLU 2.9 16.1 + - - -
783N SER* 3.6 2.5 - - - -
785N ARG* 1.3 74.2 - - - +
787N GLU* 1.3 61.9 + - - +
788N TYR 3.3 1.1 - - - -
789N ARG* 4.3 4.7 - - - +
790N ALA* 4.0 12.3 + - - -
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Residues in contact with GLU 787 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783N SER 2.8 12.1 + - - -
784N VAL* 2.7 16.6 + - - +
786N LEU* 1.3 72.9 - - - +
788N TYR* 1.3 58.5 + - - +
790N ALA* 4.3 1.3 - - - +
791N GLY 2.8 29.9 + - - +
792N LEU 4.2 4.7 - - - +
793N LYS* 5.5 0.9 - - - -
796N ALA* 5.9 6.1 - - - +
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Residues in contact with TYR 788 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784N VAL 3.0 10.3 + - - -
785N ARG 3.8 2.4 + - - -
786N LEU 3.3 0.2 - - - -
787N GLU* 1.3 76.6 - - - +
789N ARG* 1.3 66.9 + - - +
790N ALA 3.6 0.2 - - - -
791N GLY* 3.1 16.1 + - - -
793N LYS* 5.0 11.5 + - - +
796N ALA* 6.1 1.1 - - - +
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Residues in contact with ARG 789 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785N ARG 3.8 13.1 + - - -
786N LEU* 4.3 3.1 - - - +
787N GLU 3.7 0.2 - - - -
788N TYR* 1.3 74.7 - - - +
790N ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 790 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786N LEU 4.0 12.9 + - - -
787N GLU 4.6 0.2 - - - -
788N TYR 3.2 0.8 - - - -
789N ARG* 1.3 79.3 - - - +
791N GLY* 1.3 57.1 + - - +
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Residues in contact with GLY 791 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787N GLU* 2.8 17.9 + - - +
788N TYR 3.1 11.1 + - - -
790N ALA* 1.3 77.9 - - - +
792N LEU* 1.3 64.6 + - - +
793N LYS 3.3 2.2 - - - -
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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
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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