Contacts of the helix formed by residues 785 - 800 (chain A) in PDB entry 2N8Z
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 ASP 785 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781A ASP* 4.1 19.8 - - - +
783A GLY* 3.1 20.0 + - - +
784A ASN* 1.3 81.5 - - - +
786A PRO* 1.3 70.5 - - + +
787A GLN* 4.3 4.0 - - + +
788A GLY* 4.1 10.5 - - - +
789A GLU* 2.9 30.2 + - - +
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Residues in contact with PRO 786 (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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784A ASN 4.5 2.2 - - - +
785A ASP* 1.3 88.3 - - + +
787A GLN* 1.3 79.0 + - + +
789A GLU* 3.7 8.5 + - + +
790A ALA* 3.2 23.7 + - - +
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Residues in contact with GLN 787 (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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781A ASP 6.0 0.2 - - - +
785A ASP* 3.2 4.2 - - + +
786A PRO* 1.3 97.3 + - + +
788A GLY* 1.3 66.3 + - - +
790A ALA* 3.2 17.2 + - - +
791A GLU* 3.2 20.2 + - - +
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Residues in contact with GLY 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A LYS* 5.6 0.4 - - - -
781A ASP 3.9 12.8 + - - -
782A ILE* 3.4 20.8 - - - +
785A ASP* 3.2 11.1 + - - +
787A GLN* 1.3 80.7 - - - +
789A GLU* 1.3 56.3 + - - +
791A GLU* 3.2 16.7 + - - +
792A PHE* 2.8 30.5 + - - +
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Residues in contact with GLU 789 (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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772A LYS* 2.8 31.7 + - + +
783A GLY 5.7 0.2 - - - +
784A ASN* 5.2 8.1 - - - +
785A ASP 2.9 26.8 + - - +
786A PRO* 3.8 10.1 - - + +
788A GLY* 1.3 76.6 - - - +
790A ALA* 1.3 56.3 + - - +
792A PHE* 3.6 15.4 - - - -
793A ALA* 3.0 29.3 + - - +
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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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786A PRO 3.2 12.7 + - - +
787A GLN* 3.2 15.5 + - - +
789A GLU* 1.3 81.1 - - - +
791A GLU* 1.3 58.4 + - - +
793A ALA* 3.5 16.7 - - - +
794A ARG* 3.6 12.1 - - - +
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Residues in contact with GLU 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A ASP* 4.6 3.3 - - - +
782A ILE* 3.5 33.4 - - + +
787A GLN* 3.2 15.6 + - - +
788A GLY* 3.2 17.1 - - - +
790A ALA* 1.3 73.5 - - - +
792A PHE* 1.3 66.5 + - - +
793A ALA 3.1 1.6 - - - -
794A ARG* 3.0 24.3 + - + +
795A ILE* 3.2 17.8 + - + +
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Residues in contact with PHE 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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768A PRO* 3.4 41.3 - - + -
769A GLU 5.2 0.2 - - - -
772A LYS* 3.6 37.5 - - + -
775A LEU* 6.4 0.7 - - + -
782A ILE* 3.9 12.8 - - + -
788A GLY 2.8 18.5 + - - +
789A GLU* 3.6 18.2 - - + +
791A GLU* 1.3 78.1 - - - +
793A ALA* 1.3 61.4 + - + +
795A ILE* 3.0 18.4 + - + +
796A MET* 2.9 61.7 + - + +
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Residues in contact with ALA 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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789A GLU 3.0 17.2 + - - +
790A ALA* 3.5 11.7 - - - +
791A GLU 3.1 0.2 - - - -
792A PHE* 1.3 81.8 - - + +
794A ARG* 1.3 57.7 + - + +
796A MET* 3.4 27.1 - - + +
797A SER* 2.9 23.6 + - - -
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Residues in contact with ARG 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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790A ALA 3.6 15.3 - - - +
791A GLU* 3.0 18.1 + - + +
793A ALA* 1.3 77.3 - - - +
795A ILE* 1.3 68.2 + - + +
797A SER* 3.3 14.3 + - - -
798A ILE* 3.3 24.6 + - + +
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Residues in contact with ILE 795 (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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775A LEU* 4.5 14.1 - - + -
780A TYR* 6.0 1.3 - - + -
782A ILE* 4.2 25.1 - - + -
791A GLU* 3.5 15.7 - - + +
792A PHE* 3.0 18.8 + - + +
794A ARG* 1.3 79.8 - - + +
796A MET* 1.3 68.4 + - - +
798A ILE* 3.0 21.7 + - + +
799A VAL* 3.1 17.7 + - + +
807A VAL* 6.2 0.4 - - + -
815A PHE* 3.4 44.2 - - + -
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Residues in contact with MET 796 (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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768A PRO* 5.2 8.3 - - + -
792A PHE* 2.9 48.4 + - + +
793A ALA* 3.4 30.1 - - + +
795A ILE* 1.3 78.1 - - - +
797A SER* 1.3 64.3 + - - +
799A VAL* 3.8 10.8 - - + -
800A ASP* 3.1 34.3 + - + +
807A VAL* 5.7 2.5 - - + -
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Residues in contact with SER 797 (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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793A ALA 2.9 15.4 + - - -
794A ARG* 3.3 11.8 + - - -
795A ILE 3.1 1.2 - - - -
796A MET* 1.3 84.2 - - - +
798A ILE* 1.3 61.5 + - - +
800A ASP 4.2 4.3 - - - -
801A PRO* 3.7 23.4 - - - +
803A ARG* 4.8 16.2 + - - +
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Residues in contact with ILE 798 (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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794A ARG* 3.3 25.4 - - + +
795A ILE* 3.0 11.1 + - + +
797A SER* 1.3 79.7 - - - +
799A VAL* 1.3 65.8 + - + +
800A ASP 3.2 4.2 + - - -
801A PRO* 3.5 11.4 - - - +
814A ASP* 4.2 21.0 - - + +
815A PHE* 4.3 26.2 - - + +
818A ARG* 4.2 19.7 - - - +
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Residues in contact with VAL 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A ILE* 3.4 17.5 - - + +
796A MET* 3.8 11.7 - - - +
798A ILE* 1.3 77.0 - - + +
800A ASP* 1.3 62.7 + - + +
801A PRO* 3.8 2.7 - - - +
802A ASN* 5.0 1.7 + - - -
806A VAL 4.6 3.3 - - - +
807A VAL* 3.5 38.5 - - + -
808A THR* 5.7 0.9 - - - +
811A ALA* 3.3 44.8 - - + +
812A PHE* 3.9 1.3 - - - -
814A ASP* 6.1 0.4 - - - -
815A PHE* 3.5 30.5 - - + -
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Residues in contact with ASP 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A MET* 3.1 21.9 + - + +
797A SER* 4.1 1.8 - - - +
799A VAL* 1.3 86.0 - - + +
801A PRO* 1.3 62.8 - - - +
802A ASN* 3.0 15.2 + - - +
803A ARG* 3.0 17.7 + - - +
804A LEU* 2.8 24.1 + - - +
805A GLY* 2.7 31.8 + - - -
806A VAL 3.6 17.9 + - - +
807A VAL* 5.2 1.3 - - + -
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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