Contacts of the helix formed by residues 1675 - 1689 (chain A) in PDB entry 6FF7
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 ASP1675 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1673A SER 3.8 2.2 - - - -
1674A HIS* 1.3 78.3 - - - +
1676A ILE* 1.3 62.1 + - - +
1677A GLU* 3.2 4.5 - - + +
1678A ARG* 3.3 7.9 + - + +
1679A TYR* 3.0 19.9 + - - +
122t LEU 3.3 10.2 + - - +
123t ASP* 4.2 1.5 - - - +
124t THR* 3.9 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1674A HIS 4.2 0.2 - - - -
1675A ASP* 1.3 71.5 - - - +
1677A GLU* 1.3 60.6 + - - +
1678A ARG 3.1 1.1 - - - -
1679A TYR* 3.6 14.6 - - + -
1680A ALA* 2.9 31.4 + - - +
1704A ALA* 4.4 23.1 - - + +
1705A ILE 5.5 0.2 - - - -
1706A ASP* 4.7 20.0 - - + +
1711A LEU 5.9 0.9 - - - +
1712A HIS 5.6 1.3 - - - -
1713A SER* 3.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1677 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1644A LEU* 5.5 12.0 - - + +
1646A ALA* 6.3 2.7 - - + -
1675A ASP* 3.2 3.3 - - + -
1676A ILE* 1.3 78.2 - - - +
1678A ARG* 1.3 55.5 + - - +
1680A ALA* 5.0 0.7 - - - +
1681A ARG* 3.6 18.9 + - - +
1713A SER* 4.1 12.5 - - - -
1714A ALA 5.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1678 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1675A ASP* 3.3 11.8 + - + +
1677A GLU* 1.3 80.0 - - - +
1679A TYR* 1.3 58.1 - - - +
1680A ALA 3.4 0.2 - - - -
1681A ARG* 3.7 4.9 - - - +
1682A ALA* 2.9 24.9 + - - +
121t GLU* 3.1 18.4 - - + +
123t ASP 3.3 27.4 - - - +
124t THR* 5.0 2.5 - - - -
125t GLU* 5.4 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1679 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1675A ASP 3.0 13.5 + - - +
1676A ILE* 3.5 13.2 + - + -
1678A ARG* 1.3 77.2 - - - +
1680A ALA* 1.3 56.4 + - - +
1682A ALA* 3.9 1.0 - - - +
1683A LYS* 2.9 32.2 + - - +
1704A ALA* 5.2 3.6 - - + -
122t LEU* 3.2 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1680 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1676A ILE* 2.9 19.5 + - - +
1677A GLU* 5.0 1.3 - - - +
1679A TYR* 1.3 76.6 - - - +
1681A ARG* 1.3 58.3 + - - +
1683A LYS* 3.5 5.6 + - - +
1684A PHE* 2.9 31.0 + - - +
1702A LEU* 4.3 9.4 - - - +
1704A ALA* 3.7 24.1 - - + +
1713A SER* 4.9 0.4 - - - -
1714A ALA* 4.3 15.3 - - - +
1715A TYR* 3.9 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1681 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1677A GLU 3.6 18.9 + - - +
1678A ARG* 3.4 7.9 + - - +
1679A TYR 3.3 0.4 - - - -
1680A ALA* 1.3 79.2 - - - +
1682A ALA* 1.3 57.1 + - - +
1684A PHE* 3.3 2.4 + - - +
1685A LEU* 2.9 30.1 + - - +
1715A TYR* 4.0 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1678A ARG 2.9 18.6 + - - +
1679A TYR 4.0 2.5 - - - +
1681A ARG* 1.3 75.2 - - - +
1683A LYS* 1.3 56.6 + - - +
1685A LEU* 3.5 6.0 + - - +
1686A ASP* 2.9 29.5 + - - +
121t GLU* 3.4 32.8 - - + +
122t LEU* 4.2 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1679A TYR 2.9 19.3 + - - +
1680A ALA* 3.9 5.4 - - - +
1682A ALA* 1.3 77.2 - - - +
1684A PHE* 1.3 57.6 + - - +
1686A ASP* 3.3 6.8 + - - +
1687A TYR* 2.9 30.1 + - - +
1702A LEU* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680A ALA 2.9 17.9 + - - +
1681A ARG 3.9 3.1 - - - +
1683A LYS* 1.3 74.3 - - - +
1685A LEU* 1.3 61.4 + - - +
1687A TYR* 3.4 4.6 + - - +
1688A THR* 2.9 32.7 + - - -
1702A LEU* 4.1 15.8 - - + +
1715A TYR* 4.0 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1681A ARG 2.9 17.2 + - - +
1682A ALA* 3.8 6.5 - - - +
1684A PHE* 1.3 77.9 - - - +
1686A ASP* 1.3 56.2 + - - +
1688A THR* 3.8 4.1 - - - +
1689A THR* 3.0 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1682A ALA 2.9 18.9 + - - +
1683A LYS* 3.7 7.4 - - - +
1684A PHE 3.3 0.2 - - - -
1685A LEU* 1.3 77.0 - - - +
1687A TYR* 1.3 57.4 + - - +
1689A THR* 3.5 3.3 + - - -
1690A ASP* 2.9 27.7 + - - +
2s SER* 5.1 14.4 - - - -
3s ASN 5.8 1.3 - - - +
4s ILE* 4.1 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1625A SER* 5.4 12.6 - - - -
1683A LYS 2.9 16.7 + - - +
1684A PHE* 4.3 3.8 - - - +
1686A ASP* 1.3 76.8 - - - +
1688A THR* 1.3 61.3 + - - +
1690A ASP* 3.7 18.6 + - + +
1693A SER* 4.1 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1684A PHE 2.9 18.9 + - - -
1685A LEU* 3.8 4.7 - - - -
1686A ASP 3.3 0.2 - - - -
1687A TYR* 1.3 75.5 - - - +
1689A THR* 1.3 59.0 + - - +
1690A ASP 3.4 3.8 - - - +
1698A PRO* 5.1 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1685A LEU 3.0 18.3 + - - -
1686A ASP* 3.6 3.8 - - - -
1688A THR* 1.3 75.7 - - - +
1690A ASP* 1.3 62.7 + - - +
1691A ASN* 3.9 0.9 + - - +
4s ILE* 5.6 1.7 - - - +
6s ILE* 5.5 6.4 - - - +
----------------------------------------------------------
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