Contacts of the helix formed by residues 609 - 617 (chain A) in PDB entry 6FEQ
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 THR 609 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A LEU 5.0 0.2 + - - -
589A GLN 3.3 14.2 + - - -
590A ASN* 3.6 12.9 + - - +
591A PHE* 4.3 9.2 - - - -
597A ALA* 5.1 5.6 - - + +
598A THR* 5.0 10.4 - - - -
607A THR* 3.4 5.3 + - - +
608A CYS* 1.3 80.1 - - - +
610A GLY* 1.3 70.5 + - - +
611A GLU* 2.8 22.6 + - + +
612A GLU* 3.4 37.6 + - + +
613A TYR* 3.4 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A PHE* 3.2 30.8 - - - +
587A LEU 4.8 0.2 - - - -
589A GLN 3.4 11.9 + - - -
591A PHE* 4.3 14.1 - - - -
609A THR* 1.3 80.2 + - - +
611A GLU* 1.3 58.1 + - - -
613A TYR* 3.3 6.0 + - - +
614A LEU* 2.8 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A PHE 5.3 0.2 - - - +
587A LEU* 2.9 32.0 - - + +
598A THR* 5.1 5.3 + - - -
609A THR* 2.8 31.5 + - + +
610A GLY* 1.3 77.3 - - - +
612A GLU* 1.3 52.7 + - - +
614A LEU* 2.7 9.0 + - - +
615A VAL* 2.6 37.6 + - - +
621A LEU* 4.0 28.0 - - + -
30E LEU* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A ALA* 5.4 2.3 - - - +
601A ASN* 2.6 37.5 + - - +
607A THR* 3.8 12.5 - - - +
608A CYS* 3.4 20.1 + - - -
609A THR* 3.4 21.9 + - + +
610A GLY 3.4 0.4 - - - -
611A GLU* 1.3 76.2 - - - +
613A TYR* 1.3 61.2 + - - +
615A VAL 4.6 0.2 - - - +
616A LYS* 3.3 31.2 + - - +
30E LEU* 3.7 27.6 - - + +
32E ARG* 3.1 24.3 + - - +
92E TRP* 4.2 8.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ILE* 3.7 28.5 - - + -
427A ALA* 3.7 12.4 - - + +
553A GLY 5.3 0.7 + - - -
554A LEU* 4.8 8.1 - - - +
582A GLN* 3.4 30.5 + - - -
586A PHE* 4.1 32.1 - + + -
591A PHE* 6.2 0.4 - - + -
607A THR* 3.7 21.6 - - + +
609A THR 3.4 8.0 + - - +
610A GLY* 3.3 9.3 + - - +
611A GLU 3.1 0.4 - - - -
612A GLU* 1.3 78.7 - - - +
614A LEU* 1.3 66.5 + - + +
616A LYS* 3.4 7.3 + - + +
617A GLN* 3.3 56.9 + - + +
424B GLN* 4.8 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A GLN* 3.8 35.4 - - + +
583A HIS* 4.0 22.9 - - - +
586A PHE* 4.4 15.3 - - + +
587A LEU* 4.5 10.8 - - + -
610A GLY 2.8 14.2 + - - +
611A GLU* 2.7 14.3 + - - +
613A TYR* 1.3 75.3 - - + +
615A VAL* 1.3 62.1 + - - +
617A GLN* 3.8 1.1 + - - +
618A GLY 3.8 2.6 + - - -
619A ILE* 3.2 58.0 + - + +
621A LEU* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A THR* 4.9 1.6 - - - +
611A GLU 2.6 22.2 + - - +
614A LEU* 1.3 72.9 - - - +
616A LYS* 1.3 55.3 + - - +
617A GLN 3.1 0.2 - - - -
618A GLY* 2.6 26.7 + - - -
619A ILE 4.2 7.6 - - - +
621A LEU* 3.9 28.0 - - + -
28E TYR* 4.1 25.6 - - + +
30E LEU* 3.7 20.4 - - + -
92E TRP* 3.6 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASN* 3.4 25.3 + - - +
559A THR* 4.1 8.0 + - - +
605A TYR* 6.0 5.0 - - - +
606A ALA 6.1 0.4 - - - +
607A THR* 4.0 19.3 + - + +
612A GLU* 3.3 30.1 + - - +
613A TYR* 3.4 8.9 + - + +
614A LEU 3.4 0.4 - - - -
615A VAL* 1.3 77.7 - - - +
617A GLN* 1.3 65.2 + - + +
618A GLY 3.2 0.7 + - - -
420B SER* 3.4 34.1 - - - +
421B THR* 4.6 9.9 - - + -
424B GLN* 6.0 0.9 - - - +
32E ARG* 5.6 2.6 - - - +
92E TRP* 3.7 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A GLY* 2.9 26.4 - - - +
557A ASN* 3.5 14.8 + - - +
558A LEU* 4.3 17.5 + - - +
559A THR* 4.1 6.4 - - - +
578A PHE* 5.9 0.2 - - - -
582A GLN* 4.8 5.7 + - - +
613A TYR* 3.3 53.0 + - + +
614A LEU* 4.1 2.0 - - + +
615A VAL 3.1 1.0 - - - -
616A LYS* 1.3 81.8 - - - +
618A GLY* 1.3 61.6 + - - +
619A ILE* 4.1 21.4 - - + +
424B GLN* 2.9 34.2 + - - +
----------------------------------------------------------
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