Contacts of the helix formed by residues 715 - 722 (chain A) in PDB entry 2NUP
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 715 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TYR* 3.9 18.8 - - + +
708A THR* 3.2 21.6 + - - +
709A GLU 3.9 10.5 - - - +
710A HIS* 5.1 0.2 - - - -
711A GLY 4.8 3.6 - - - +
712A GLY 3.3 17.0 - - - +
713A SER 3.1 0.6 - - - -
714A GLN* 1.3 77.7 - - - +
716A ARG* 1.3 61.5 + - - +
717A PHE 3.2 0.2 - - - -
718A LEU* 3.1 17.5 + - - +
719A LEU* 3.3 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 716 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A SER* 3.1 23.8 + - - +
714A GLN* 3.0 1.2 - - - +
715A ALA* 1.3 78.3 - - - +
717A PHE* 1.3 100.1 + - + +
719A LEU* 3.3 13.4 + - + +
720A SER* 2.9 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 717 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A MET* 3.4 3.3 - - - +
655A GLN* 3.2 29.6 + - - +
657A LEU* 3.5 17.9 - - + -
704A ARG* 3.4 27.6 - - - -
706A ILE* 4.2 15.7 - - + -
714A GLN* 3.2 29.2 - - + -
715A ALA 3.2 1.2 - - - -
716A ARG* 1.3 115.6 - - + +
718A LEU* 1.3 61.2 + - - +
720A SER* 3.1 15.2 + - - -
721A LYS* 3.3 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 718 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LEU* 3.9 31.4 - - + -
637A LEU* 5.5 0.9 - - + -
642A ILE* 4.4 18.6 - - + -
648A LEU* 4.0 14.6 - - + -
650A MET* 3.4 23.9 - - + +
657A LEU* 4.2 10.6 - - + +
659A TYR* 3.6 44.9 - - + -
715A ALA 3.1 10.3 + - - +
717A PHE* 1.3 80.2 - - - +
719A LEU* 1.3 64.6 + - + +
720A SER 3.1 1.4 + - - -
721A LYS* 3.1 3.5 + - - +
722A VAL* 3.1 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 719 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ILE* 3.6 29.6 - - + -
659A TYR* 5.7 4.7 - - + +
715A ALA* 3.3 28.2 + - + +
716A ARG* 3.3 11.6 + - + +
718A LEU* 1.3 80.0 - - + +
720A SER* 1.3 57.2 + - - +
721A LYS 3.5 0.2 - - - -
722A VAL* 3.0 23.7 - - + +
723A ASN* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 720 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ARG* 3.2 24.3 + - - -
716A ARG 2.9 17.8 + - - -
717A PHE* 3.1 13.9 + - - -
719A LEU* 1.3 76.1 - - - +
721A LYS* 1.3 65.7 + - - +
722A VAL 3.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 721 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A HIS* 4.4 7.1 + - - -
586A ARG* 4.8 2.7 + - - +
587A SER* 5.5 4.4 - - - +
588A SER* 4.9 19.0 - - - +
618A MET 5.0 9.3 + - - -
621A PRO* 4.2 18.8 - - + +
637A LEU* 3.6 22.1 - - + +
650A MET* 3.8 28.0 - - + -
652A THR* 4.2 23.7 - - - +
654A PHE* 6.3 0.4 - - - -
655A GLN* 4.9 7.2 - - - +
717A PHE 3.3 16.6 - - - +
718A LEU 3.1 1.4 + - - +
720A SER* 1.3 81.2 - - - +
722A VAL* 1.3 67.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 722 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A HIS* 5.0 1.2 - - - -
586A ARG* 3.7 14.9 + - - -
623A LEU* 5.5 4.3 - - + -
637A LEU* 3.5 13.9 - - + -
638A ASP 3.0 36.8 - - - +
639A SER* 3.2 16.6 - - - +
642A ILE* 4.4 13.0 - - + -
718A LEU* 3.1 14.3 + - + +
719A LEU* 3.0 32.8 - - + +
720A SER 3.4 0.4 - - - +
721A LYS* 1.3 84.7 - - - +
723A ASN* 1.3 82.0 + - + +
----------------------------------------------------------
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