Contacts of the helix formed by residues 702 - 708 (chain A) in PDB entry 6FWF
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 GLY 702 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A HIS* 3.5 17.5 - - - -
219A PRO* 4.6 1.8 - - - -
697A ALA 3.2 4.5 + - - +
698A SER* 3.4 19.9 + - - -
700A THR 3.3 3.8 - - - -
701A HIS* 1.3 78.6 - - - +
703A LEU* 1.3 60.7 + - - -
704A TRP* 3.4 8.1 - - - -
705A TYR* 3.2 4.2 + - - +
706A ALA 2.8 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP* 5.1 1.6 - - - -
85A ALA* 4.3 8.1 - - + -
215A TRP* 3.1 44.4 - - + +
216A PRO* 4.0 9.6 - - + -
217A HIS* 3.4 26.0 + - + +
622A PHE 5.1 0.2 - - - +
623A TYR* 3.3 29.2 - - - +
625A GLN 4.3 3.8 - - - +
627A LEU* 3.6 23.3 - - + -
698A SER* 3.8 14.6 + - - -
702A GLY* 1.3 71.8 - - - -
704A TRP* 1.3 52.6 + - - +
706A ALA* 3.0 3.6 + - - +
707A ARG* 2.8 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 3.6 35.6 - - + +
86A ASP* 3.9 11.1 - - - +
89A HIS* 3.3 50.9 - + + -
108A PHE* 6.2 3.1 - + - -
217A HIS 3.7 19.1 + - - -
218A GLU* 2.7 39.5 + - - -
219A PRO* 3.8 7.3 - - + +
220A LEU* 4.4 14.6 - - + -
701A HIS* 3.2 24.7 - - + -
702A GLY* 4.1 1.0 - - - -
703A LEU* 1.3 78.5 - - - +
705A TYR* 1.3 88.3 + + + -
707A ARG* 3.5 5.8 + - - +
708A SER* 2.8 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 705 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A ALA* 4.7 4.0 - - + -
701A HIS* 3.3 50.8 + + + +
702A GLY 3.2 8.2 + - - +
703A LEU 3.2 0.6 - - - -
704A TRP* 1.3 101.3 - + + +
706A ALA* 1.3 67.3 + - - +
707A ARG 3.1 1.6 - - - -
708A SER* 2.7 30.3 + - - -
710A GLU* 4.9 20.2 + - + +
711A PHE* 3.1 47.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A LEU* 4.8 3.6 - - + -
694A GLN* 3.4 31.6 + - + +
697A ALA* 4.0 4.5 - - + -
698A SER* 3.5 35.0 - - - +
702A GLY 2.8 12.0 + - - +
703A LEU* 3.4 9.0 - - - +
705A TYR* 1.3 73.1 - - - +
707A ARG* 1.3 57.0 + - - +
711A PHE* 3.2 28.5 - - - -
712A LEU* 4.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 707 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 3.0 27.9 + - - -
77A ALA 3.7 1.4 + - - -
78A TYR* 3.6 28.3 + - - +
80A ALA 2.4 33.2 + - - -
81A PRO* 3.4 24.2 - - + +
82A ASP* 3.7 27.1 - - + +
86A ASP* 6.3 0.4 - - + -
626A GLY 3.9 18.3 + - - -
627A LEU* 4.4 6.1 - - - -
694A GLN* 4.0 14.0 - - - +
703A LEU* 2.8 31.4 + - + +
704A TRP* 3.6 6.1 - - - +
706A ALA* 1.3 73.8 - - - +
708A SER* 1.3 62.9 + - - +
709A GLU 3.8 0.5 + - - -
712A LEU* 3.4 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 708 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO* 4.6 6.1 - - - -
86A ASP* 5.1 7.2 - - - -
155A TYR* 6.0 1.1 - - - -
704A TRP* 2.8 21.4 + - - -
705A TYR* 2.7 30.4 + - - -
707A ARG* 1.3 76.8 - - - +
709A GLU* 1.3 59.0 + - - +
710A GLU* 4.0 7.6 + - - +
711A PHE* 3.0 16.8 + - - +
712A LEU* 2.8 30.6 + - - +
----------------------------------------------------------
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