Contacts of the helix formed by residues 669 - 678 (chain I) in PDB entry 3AOI
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 669 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662I GLU* 3.7 15.9 - - - +
667I ALA* 3.5 3.4 - - - +
668I PRO* 1.3 86.6 - - - +
670I VAL* 1.3 68.8 + - + +
671I LYS* 3.2 24.2 - - - +
672I ALA* 3.1 35.2 + - - +
673I ALA* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 670 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067H TYR* 5.0 1.8 - - - +
1071H ILE* 3.3 55.4 - - + +
658I LEU* 3.9 24.8 - - + +
659I LYS* 6.2 0.9 - - - +
662I GLU* 4.5 8.9 + - + +
669I ASN* 1.3 77.0 - - + +
671I LYS* 1.3 66.3 + - + +
673I ALA* 2.9 18.1 + - - +
674I ARG* 2.9 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 671 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669I ASN* 3.2 14.0 - - - +
670I VAL* 1.3 78.8 - - + +
672I ALA* 1.3 59.5 + - - +
674I ARG* 3.4 9.5 + - - +
675I ARG* 3.0 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 672 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667I ALA* 4.5 1.1 - - - -
668I PRO* 3.5 22.7 - - + -
669I ASN* 3.1 33.0 - - - +
670I VAL 3.0 0.4 - - - -
671I LYS* 1.3 73.2 - - - +
673I ALA* 1.3 66.8 + - - +
675I ARG* 3.2 19.2 + - - +
676I MET* 2.9 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 673 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658I LEU* 3.2 23.1 - - + +
661I MET* 3.2 34.7 - - + +
667I ALA* 3.8 12.0 - - + +
669I ASN 2.9 11.7 + - - +
670I VAL* 2.9 5.7 + - - +
672I ALA* 1.3 75.7 - - - +
674I ARG* 1.3 59.4 + - - +
676I MET* 2.9 20.6 - - - +
677I LEU* 3.1 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 674 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009H SER* 5.5 0.2 + - - -
1010H THR* 4.0 24.7 + - - +
1067H TYR* 3.9 27.3 + - - -
654I LYS* 4.0 32.2 + - - +
658I LEU* 3.6 13.1 - - + +
670I VAL* 2.9 12.4 + - + +
671I LYS* 3.5 13.2 - - - +
673I ALA* 1.3 73.5 - - - +
675I ARG* 1.3 61.2 + - + +
676I MET 3.0 1.8 - - - -
677I LEU* 2.8 22.5 + - - +
678I GLU* 3.0 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 675 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671I LYS* 3.0 20.2 + - - +
672I ALA* 3.7 13.4 + - - +
674I ARG* 1.3 76.7 - - + +
676I MET* 1.3 63.3 + - - +
678I GLU* 3.0 49.5 + - - +
679I ARG* 4.6 1.6 + - - +
682I ASP* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 676 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661I MET* 4.0 11.2 - - + -
666I ILE* 4.5 5.8 - - + +
667I ALA* 5.3 1.1 - - + -
672I ALA 2.9 14.9 + - - +
673I ALA* 2.9 20.0 - - - +
675I ARG* 1.3 80.3 - - - +
677I LEU* 1.3 57.3 + - + +
678I GLU 4.0 0.2 + - - -
679I ARG 4.1 0.7 - - - +
682I ASP* 3.5 43.4 - - - +
683I ILE* 4.7 1.8 + - - -
684I LYS* 3.2 47.3 - - + +
687I VAL* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 677 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650I LEU* 4.6 20.5 - - + +
654I LYS* 4.4 26.0 + - + +
657I LEU* 3.8 22.7 - - + -
658I LEU* 4.1 13.9 - - + -
661I MET* 3.9 11.2 - - + -
673I ALA 3.1 18.8 - - - +
674I ARG* 2.8 9.0 + - - +
676I MET* 1.3 84.8 - - + +
678I GLU* 1.3 58.1 + - - -
679I ARG 3.1 14.0 + - - +
683I ILE* 5.4 9.3 - - + +
687I VAL* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 678 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654I LYS* 5.8 1.8 - - - +
674I ARG 3.0 7.9 + - - +
675I ARG* 3.0 48.6 + - - +
677I LEU* 1.3 77.1 - - - +
679I ARG* 1.3 98.7 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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