Contacts of the helix formed by residues 687 - 695 (chain A) in PDB entry 1FGR
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 SER 687 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A HIS* 4.5 0.4 - - - -
621A ILE* 4.0 9.7 - - - +
683A ILE 2.7 24.3 + - - -
684A TRP 3.9 0.5 + - - -
685A ILE 3.4 0.4 - - - -
686A ALA* 1.3 79.9 - - - +
688A ALA* 1.3 66.9 + - - +
689A LEU 3.5 0.2 - - - -
690A HIS* 3.5 2.1 + - - +
691A ALA* 2.9 29.1 + - - +
764A LEU* 3.9 21.4 - - - +
833A ILE* 3.5 11.8 - - - +
834A PRO* 3.2 22.6 - - - +
835A ASN 3.6 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ILE* 3.9 19.1 - - + -
684A TRP* 3.3 37.5 + - + -
687A SER* 1.3 80.0 + - - +
689A LEU* 1.3 66.7 + - - +
691A ALA* 3.8 0.7 - - - +
692A ALA* 2.9 26.9 + - - +
820A LEU* 3.8 14.6 - - + +
833A ILE* 3.5 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A CYS* 5.3 7.2 - - + -
498A SER 5.5 1.8 - - - +
502A ASN* 4.6 8.5 - - + +
503A THR* 4.2 16.4 - - + -
579A GLN* 4.5 15.5 - - - +
610A TYR* 3.4 25.4 - - + +
684A TRP* 3.0 41.5 + - + +
685A ILE* 3.7 26.5 - - + +
688A ALA* 1.3 74.9 - - - +
690A HIS* 1.3 66.5 + - - +
692A ALA* 3.3 2.8 + - - +
693A VAL* 3.2 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 690 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A HIS* 3.3 8.7 + + - -
503A THR* 3.5 27.8 - - + -
504A HIS* 3.6 1.0 + - - -
685A ILE 3.2 17.0 + - - +
686A ALA 3.9 6.5 - - - +
687A SER 3.5 1.0 + - - -
688A ALA 3.3 0.2 - - - -
689A LEU* 1.3 80.0 - - - +
691A ALA* 1.3 65.6 + - - +
693A VAL* 3.3 3.1 + - - +
694A ASN* 2.9 46.2 + - + +
695A PHE* 4.4 8.4 - + - -
834A PRO* 5.6 0.8 - - - +
836A SER 4.0 6.0 + - - -
837A ILE* 3.8 34.6 - - + +
838A SER* 4.4 3.8 - - - -
839A ILE* 3.1 17.4 + - + -
840A FE 2.2 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 691 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A SER 2.9 19.1 + - - +
688A ALA 3.8 3.8 - - - +
690A HIS* 1.3 76.2 + - - +
692A ALA* 1.3 62.8 - - - +
695A PHE* 3.1 39.9 + - + +
819A LEU* 4.3 10.8 - - - +
820A LEU* 5.1 0.2 - - + -
832A GLY 3.9 22.0 - - - +
833A ILE* 4.1 13.0 - - + -
834A PRO* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 692 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLY 4.3 4.5 - - - +
354A VAL* 3.8 8.0 - - - +
356A PRO* 4.4 3.1 - - + +
610A TYR* 3.7 34.8 - - + -
688A ALA 2.9 17.7 + - - +
689A LEU 3.8 2.7 - - - +
691A ALA* 1.3 77.8 - - - +
693A VAL* 1.3 63.4 + - + +
695A PHE 5.0 0.3 + - - -
696A GLY 5.0 0.5 + - - -
817A TYR* 4.3 5.8 + - - +
819A LEU* 3.9 26.9 - - - +
820A LEU* 4.1 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 693 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 3.4 19.9 - - - +
356A PRO* 4.5 4.7 - - + -
357A CYS* 4.2 24.2 - - - -
494A HIS* 2.7 36.9 + - + +
498A SER* 3.8 24.2 - - - +
499A HIS* 4.3 16.0 + - + -
503A THR* 4.5 2.2 - - + -
610A TYR* 5.8 0.9 - - + -
689A LEU* 3.2 27.1 + - + +
690A HIS* 3.5 10.5 - - - +
692A ALA* 1.3 81.3 - - + +
694A ASN* 1.3 61.8 + - - +
697A GLU* 4.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 694 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A HIS* 3.0 28.5 + - - +
690A HIS* 2.9 36.4 + - + +
691A ALA 4.2 0.2 - - - +
693A VAL* 1.3 79.0 - - - +
695A PHE* 1.3 84.8 + - + +
696A GLY 3.0 10.0 + - - -
697A GLU* 3.1 25.8 + - - +
754A LEU* 2.8 36.9 + - - +
755A SER* 4.0 2.6 + - - -
839A ILE* 3.9 4.9 - - - +
840A FE 3.4 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A HIS* 4.4 6.5 - + - -
691A ALA* 3.1 30.0 + - + -
694A ASN* 1.3 95.7 - - + +
696A GLY* 1.3 57.2 + - - +
697A GLU 3.3 0.9 - - - -
699A PRO* 3.4 19.8 - - - +
754A LEU 3.7 7.2 - - - -
755A SER* 3.6 25.9 - - - +
756A THR 4.0 8.1 - - - -
757A HIS* 3.3 46.0 - + - +
761A GLU* 5.6 0.2 - - - -
819A LEU* 3.6 21.0 - - + +
830A PHE* 3.9 6.8 + - - +
831A ARG 5.0 6.5 - - - +
832A GLY 4.2 2.9 - - - +
834A PRO* 3.7 22.2 - - + -
838A SER* 5.4 0.9 - - - -
839A ILE* 3.7 17.9 - - + -
----------------------------------------------------------
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