Contacts of the helix formed by residues 2694 - 2705 (chain A) in PDB entry 4ERV
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 ALA2694 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2692A GLY 3.2 0.6 - - - -
2693A GLU* 1.3 79.0 - - - +
2695A LEU* 1.3 64.8 + - - +
2696A VAL 3.5 1.8 - - - -
2697A GLN* 3.4 11.5 + - - +
2698A GLN* 3.1 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2692A GLY* 3.4 21.9 + - - +
2694A ALA* 1.3 76.5 - - - +
2696A VAL* 1.3 63.1 + - + +
2698A GLN* 3.3 18.6 + - + +
2699A ARG* 2.9 66.4 + - + +
2793A VAL* 3.4 19.5 - - + +
2795A GLY 5.3 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2616A TYR* 4.0 17.5 - - + +
2617A ILE* 4.4 8.7 - - + -
2620A LYS* 4.0 34.5 - - + -
2692A GLY 4.7 2.4 + - - +
2693A GLU 5.4 0.8 + - - -
2694A ALA 3.5 0.4 - - - -
2695A LEU* 1.3 77.7 - - - +
2697A GLN* 1.3 57.9 + - - +
2699A ARG* 3.4 8.6 + - - +
2700A GLU* 3.0 26.6 + - + +
2794A ASN* 3.4 50.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2697 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2616A TYR* 4.5 12.8 + - - -
2693A GLU 5.8 0.7 - - - +
2694A ALA* 3.4 11.3 + - - +
2695A LEU 3.3 0.4 - - - -
2696A VAL* 1.3 77.1 - - - +
2698A GLN* 1.3 60.6 + - + +
2700A GLU* 3.3 11.2 + - - +
2701A ASN* 2.9 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2698 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2694A ALA* 3.1 31.9 + - + +
2695A LEU* 3.3 31.8 + - + +
2697A GLN* 1.3 75.0 - - + +
2699A ARG* 1.3 58.0 + - - +
2701A ASN* 3.4 9.7 + - - +
2702A GLU* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2695A LEU* 2.9 46.3 + - + +
2696A VAL* 3.7 7.5 - - - +
2698A GLN* 1.3 77.2 - - - +
2700A GLU* 1.3 56.4 + - - +
2702A GLU* 3.3 7.9 + - + +
2703A LYS* 3.0 28.3 + - - +
2721A LEU* 3.5 47.0 - - + +
2793A VAL* 3.0 37.2 + - - +
2794A ASN* 3.5 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2700 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2616A TYR* 5.7 2.0 - - - +
2620A LYS* 5.0 15.0 - - - -
2696A VAL 3.0 15.8 + - - +
2697A GLN* 3.3 16.4 + - - +
2699A ARG* 1.3 74.3 - - - +
2701A ASN* 1.3 65.0 + - - +
2703A LYS* 3.3 8.2 + - - +
2704A LEU* 3.2 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2697A GLN* 2.9 48.2 + - - +
2698A GLN* 3.7 8.9 - - - +
2700A GLU* 1.3 75.4 - - - +
2702A GLU* 1.3 61.8 + - - +
2704A LEU* 3.3 9.5 + - - +
2705A ARG* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2698A GLN 2.9 18.5 + - - +
2699A ARG* 3.7 7.6 - - + +
2700A GLU 3.2 0.2 - - - -
2701A ASN* 1.3 74.1 - - - +
2703A LYS* 1.3 66.5 + - - +
2704A LEU 3.2 1.0 + - - -
2705A ARG* 2.7 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2699A ARG 3.0 14.4 + - - +
2700A GLU* 3.5 12.8 - - - +
2702A GLU* 1.3 77.4 - - - +
2704A LEU* 1.3 66.0 + - + +
2705A ARG 3.7 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2700A GLU* 3.2 19.5 + - + +
2701A ASN* 3.8 7.9 - - - +
2702A GLU 3.1 0.8 - - - -
2703A LYS* 1.3 80.6 - - + +
2705A ARG* 1.3 65.2 + - - +
2706A SER* 3.4 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2705 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2701A ASN 3.1 12.8 + - - +
2702A GLU* 2.7 55.4 + - - +
2703A LYS 4.2 3.6 - - - +
2704A LEU* 1.3 76.9 - - - +
2706A SER* 1.3 63.9 - - - +
2707A VAL* 3.9 26.3 - - - +
----------------------------------------------------------
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