Contacts of the helix formed by residues 708 - 716 (chain A) in PDB entry 2XAF
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 ALA 708 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ALA 4.6 2.7 - - - +
537A GLU* 4.4 0.7 - - - +
538A PHE* 3.7 38.4 - - + +
658A ASN 5.6 0.2 - - - +
659A LEU* 4.8 11.0 - - + -
689A GLY* 3.2 18.5 + - - +
692A PHE* 4.3 11.9 - - + -
706A LEU* 4.1 0.4 - - + -
707A VAL* 1.3 75.5 - - - +
709A GLY* 1.3 70.5 + - - +
711A ALA* 3.4 10.7 + - - +
712A ALA* 3.3 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 709 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A GLU* 3.6 33.5 + - - +
542A THR* 4.6 3.2 - - - +
543A PRO* 4.0 17.2 - - - +
658A ASN 5.0 4.2 + - - +
689A GLY* 5.1 2.0 - - - -
708A ALA* 1.3 80.9 - - - +
710A GLU* 1.3 64.2 + - - +
711A ALA 3.1 0.2 + - - -
712A ALA* 3.2 13.1 + - - +
713A GLY 4.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A GLU* 4.0 7.4 + - - +
543A PRO* 3.3 35.1 - - + +
545A SER* 4.6 4.5 + - - -
686A ALA 4.5 13.5 - - - +
689A GLY* 5.8 0.8 - - - +
709A GLY* 1.3 71.7 - - - +
711A ALA* 1.3 60.8 + - - +
712A ALA 3.3 0.7 + - - -
713A GLY* 3.6 6.9 + - - -
714A ILE* 3.5 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A ALA 4.9 6.9 + - - +
687A SER* 5.3 1.3 - - - -
689A GLY* 3.9 5.2 - - - +
690A GLU* 3.5 40.4 - - + +
707A VAL* 3.9 5.4 - - + -
708A ALA 3.4 10.7 + - - +
709A GLY 3.1 0.2 - - - -
710A GLU* 1.3 79.3 - - - +
712A ALA* 1.3 57.1 + - - +
714A ILE* 3.0 12.9 + - - +
715A MET* 2.8 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A ASN* 4.4 14.1 - - + +
659A LEU* 4.2 14.8 - - - -
660A ASN* 3.5 8.9 + - - +
707A VAL* 3.4 32.5 - - - +
708A ALA* 3.3 6.7 + - - -
709A GLY 3.2 13.6 + - - +
711A ALA* 1.3 78.6 - - - +
713A GLY* 1.3 62.8 - - - +
715A MET* 3.5 6.9 + - - +
716A GLU* 3.5 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 713 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A ASN* 4.2 14.6 - - - +
709A GLY 4.3 1.4 + - - -
710A GLU 3.6 6.5 + - - -
711A ALA 3.3 0.8 - - - -
712A ALA* 1.3 78.9 - - - +
714A ILE* 1.3 61.1 + - - +
716A GLU* 3.5 16.2 + - - +
717A ASN* 4.4 3.8 + - - +
752A ARG* 5.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 714 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A ALA 6.0 1.8 - - - +
710A GLU* 3.5 25.8 - - + +
711A ALA* 3.0 8.0 + - - +
713A GLY* 1.3 73.8 - - - +
715A MET* 1.3 67.1 + - + +
717A ASN* 3.2 22.7 + - + +
718A ILE* 4.3 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 715 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A ASN* 5.7 2.2 - - + +
690A GLU* 3.6 22.0 - - + +
691A LEU* 3.9 28.9 - - + -
707A VAL* 3.7 25.4 - - + -
711A ALA* 2.8 21.9 + - + +
712A ALA 3.9 5.4 - - - +
713A GLY 3.4 0.4 - - - -
714A ILE* 1.3 72.3 - - + +
716A GLU* 1.3 62.1 + - - +
717A ASN 2.9 6.8 + - - -
718A ILE* 3.0 33.9 + - - +
723A ILE* 3.5 41.1 - - + +
726A ARG* 3.8 23.1 - - - +
750A ARG* 4.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 716 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A ASN* 3.4 3.6 + - - -
660A ASN* 3.0 32.2 + - - +
712A ALA 3.5 6.7 + - - +
713A GLY* 3.5 10.3 + - - +
714A ILE 3.2 1.2 - - - -
715A MET* 1.3 77.4 - - - +
717A ASN* 1.3 60.4 + - - +
718A ILE 3.3 2.9 + - - -
750A ARG* 2.9 45.4 + - + +
751A TRP 3.1 2.8 + - - -
752A ARG* 2.9 32.9 + - - +
753A ALA* 2.9 31.4 + - + +
----------------------------------------------------------
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