Contacts of the helix formed by residues 477 - 490 (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 PRO 477 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.7 26.2 - - + -
55A LEU* 5.3 1.8 - - + -
475A LYS 4.5 1.8 - - - +
476A SER* 1.4 87.7 - - - +
478A ILE* 1.3 63.8 + - - +
479A ALA* 3.5 3.9 + - + +
480A VAL* 3.6 20.2 + - + +
481A MET* 3.3 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.5 12.6 + - - +
58A GLN* 4.1 13.0 - - + +
61A TRP* 4.7 9.6 - - - +
62A GLN* 4.7 2.2 - - - +
67A MET* 5.8 5.6 - - + -
72A VAL* 5.6 2.5 - - + -
73A LEU* 4.5 25.6 - - + -
192A PHE* 3.9 27.8 - - + -
195A TRP* 4.3 21.3 - - + -
410A TYR* 5.7 2.5 - - + -
472A TYR* 5.8 0.2 - - - +
476A SER 3.7 0.2 + - - -
477A PRO* 1.3 70.7 - - - +
479A ALA* 1.3 65.2 + - + +
481A MET* 3.3 23.6 - - + +
482A GLU* 2.8 40.8 + - + +
546A SER* 5.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 4.0 18.6 - - + +
32A LYS 5.5 2.5 - - - +
477A PRO* 3.5 2.2 - - + +
478A ILE* 1.3 83.6 - - + +
480A VAL* 1.3 53.6 + - + +
482A GLU* 3.3 4.8 + - - +
483A TYR* 2.8 36.5 + - - +
543A LEU* 5.2 1.6 - - - +
546A SER* 3.8 24.7 - - - +
547A GLY* 5.3 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL 4.0 4.0 - - - +
30A TYR* 3.7 59.0 - - + +
471A PHE 5.2 1.3 - - - +
476A SER* 6.3 1.3 - - - -
477A PRO* 3.6 21.7 + - + +
479A ALA* 1.3 75.0 - - + +
481A MET* 1.3 54.3 + - + +
483A TYR* 3.3 10.8 + - + +
484A TRP* 2.8 55.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 3.0 24.2 - - - +
62A GLN* 3.1 28.0 - - - +
410A TYR* 3.4 26.2 - - + +
471A PHE 5.4 1.1 - - - -
472A TYR* 2.9 41.3 - - + +
473A GLY 3.4 14.8 - - - +
476A SER* 3.1 20.4 - - - +
477A PRO 3.3 11.6 + - - +
478A ILE* 3.3 18.2 - - + +
479A ALA 3.2 0.2 - - - -
480A VAL* 1.3 81.5 - - + +
482A GLU* 1.3 57.8 + - - +
484A TRP* 3.3 2.3 + - - -
485A ARG 2.8 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A MET* 3.3 26.3 - - + +
73A LEU* 4.8 11.6 - - - +
75A HIS* 2.7 41.1 + - - +
472A TYR* 4.6 6.1 - - - +
478A ILE* 2.8 28.8 + - + +
479A ALA* 3.9 4.0 - - - +
481A MET* 1.3 71.0 - - - +
483A TYR* 1.3 59.4 + - - +
485A ARG* 3.0 15.8 + - - +
486A TRP* 2.8 49.8 + - + -
543A LEU* 4.7 2.2 - - + +
546A SER* 3.7 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.7 15.9 + - + -
23A GLY* 4.3 6.4 + - - -
26A GLY* 3.3 36.6 - - - -
29A VAL* 3.6 28.0 - - + -
30A TYR* 5.8 2.7 - + + -
479A ALA 2.8 20.8 + - - +
480A VAL* 3.3 15.7 - - + +
482A GLU* 1.3 70.7 - - - +
484A TRP* 1.3 99.2 + + - +
486A TRP* 3.5 1.6 + - - +
487A TRP* 2.8 70.5 + + - +
540A LEU* 4.7 3.3 - - + +
543A LEU* 3.7 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 5.4 3.6 - - - -
468A PRO* 3.3 58.3 - - + +
469A GLY* 3.8 4.7 - - - -
471A PHE* 3.3 46.5 + + + +
472A TYR* 4.4 6.3 - - + -
480A VAL* 2.8 42.0 + - + +
481A MET 3.5 4.5 - - - +
483A TYR* 1.3 100.4 - + - +
485A ARG* 1.3 60.2 + - - +
487A TRP* 3.4 48.1 - + - +
488A VAL 3.7 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A MET* 3.8 25.8 - - - +
75A HIS* 4.1 9.1 - - - +
410A TYR* 3.8 19.7 - - - -
411A GLU* 2.8 45.2 + - - +
412A TYR* 3.4 20.0 - - - -
413A LEU* 3.8 22.4 - - + -
472A TYR* 3.8 11.4 - - + -
481A MET 2.8 16.8 + - - +
482A GLU* 3.0 18.4 + - - +
484A TRP* 1.3 69.6 - - - +
486A TRP* 1.3 94.7 + - - +
487A TRP 3.1 0.9 - - - -
488A VAL* 2.8 22.5 + - - +
489A VAL* 2.8 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 4.2 19.6 - + - -
411A GLU* 4.6 0.4 - - - -
412A TYR* 4.6 3.8 - + - -
482A GLU* 2.8 40.8 + - + +
483A TYR 4.5 0.9 - - - +
485A ARG* 1.3 108.7 - - + +
487A TRP* 1.3 61.3 + - - +
489A VAL* 3.3 30.3 - - + -
490A HIS* 3.2 21.3 + + + -
491A LEU* 3.5 3.5 + - - +
539A THR* 3.4 19.8 + - + +
542A HIS* 3.4 48.1 - + + +
543A LEU* 3.3 30.9 - - + +
1001A HEM 3.3 47.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 4.4 22.7 - + - -
22A LEU* 3.3 32.8 - - + +
23A GLY* 5.2 3.1 - - - -
465A PHE* 4.1 24.5 - + - +
468A PRO* 3.5 30.8 - - + +
483A TYR* 2.8 70.1 + + - +
484A TRP* 3.4 37.5 - + + +
486A TRP* 1.3 75.2 - - - +
488A VAL* 1.3 58.7 + - - +
491A LEU* 3.2 36.0 - - + +
492A TRP 4.1 1.4 + - - -
539A THR* 5.5 1.5 - - + +
540A LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU* 4.0 23.3 - - + -
420A GLN* 5.5 0.2 - - - +
465A PHE 3.5 20.0 - - - +
466A TYR* 3.6 24.7 - - + +
468A PRO* 3.8 1.3 - - + -
469A GLY* 3.2 40.6 - - - +
484A TRP 3.7 0.4 + - - +
485A ARG 2.8 23.1 + - - +
487A TRP* 1.3 75.2 - - - +
489A VAL* 1.3 63.6 + - + +
490A HIS 3.2 2.2 - - - -
491A LEU 3.8 0.2 - - - -
492A TRP* 2.9 32.2 + - + +
493A VAL* 3.4 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A TYR* 3.4 44.0 - - + -
413A LEU* 5.0 1.1 - - + -
485A ARG* 2.8 37.0 + - + +
486A TRP* 3.3 36.7 - - + -
488A VAL* 1.3 77.2 - - + +
490A HIS* 1.3 59.4 + - - +
493A VAL* 3.5 24.2 - - + +
1001A HEM 5.9 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A TRP* 3.2 15.1 + + + +
489A VAL* 1.3 78.7 - - - +
491A LEU* 1.3 62.3 + - - +
493A VAL* 4.9 0.2 - - - -
494A GLU* 3.2 36.0 - - + +
535A GLY* 4.5 3.5 + - - +
539A THR* 3.3 25.7 + - - +
541A HIS* 3.1 20.3 + + - -
542A HIS* 3.1 15.8 - + + -
563A GLU* 3.8 13.0 - - - -
1001A HEM 3.5 37.2 + + + -
1004A FE 1.9 29.0 - - - -
----------------------------------------------------------
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