Contacts of the helix formed by residues 563 - 579 (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 GLU 563 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A HIS* 3.8 16.9 - - - -
494A GLU* 4.6 2.3 - - - +
531A PHE* 4.3 14.1 - - + -
534A GLY* 3.3 24.7 - - - +
535A GLY* 3.5 14.6 - - - -
538A GLY* 3.3 32.7 - - - -
539A THR 3.6 1.6 + - - -
541A HIS* 3.3 16.5 + - - -
559A PHE 2.8 11.8 + - - +
560A SER* 3.3 12.5 - - - +
561A ALA 3.2 0.6 - - - -
562A LEU* 1.3 73.6 - - - +
564A VAL* 1.3 58.8 + - - +
566A PRO* 3.4 12.4 - - - +
567A LEU* 3.8 21.3 - - - +
1001A HEM 3.9 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.8 20.0 - - + -
244A ILE* 6.0 0.9 - - + -
560A SER 3.8 1.1 - - - +
561A ALA 3.1 16.2 + - - +
563A GLU* 1.3 78.0 - - - +
565A VAL* 1.3 59.5 + - - +
567A LEU* 3.0 7.5 + - - +
568A VAL* 2.8 39.5 + - + +
609A GLY* 3.8 21.1 - - - +
610A VAL* 6.0 1.6 - - + -
613A PHE* 3.8 23.6 - - + -
1001A HEM 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 4.0 13.9 - - + +
243A GLY* 4.6 5.2 - - - -
244A ILE* 4.2 27.4 - - + +
247A LEU* 3.7 29.8 - - + -
530A ILE* 6.3 1.1 - - + -
562A LEU* 3.6 22.4 + - + +
564A VAL* 1.3 78.4 - - - +
566A PRO* 1.4 71.9 - - + +
568A VAL* 3.6 12.8 - - + +
569A LEU* 3.1 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLU* 5.8 1.1 - - - +
527A ALA* 6.0 0.9 - - + -
530A ILE* 3.8 49.6 - - + +
531A PHE* 4.5 17.0 - - + -
562A LEU 3.2 18.4 - - - +
563A GLU* 3.4 12.6 - - - +
565A VAL* 1.4 94.6 - - + +
567A LEU* 1.3 63.9 + - + +
568A VAL 3.3 0.2 - - - -
569A LEU* 3.2 22.4 + - + +
570A LEU* 4.1 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLU* 4.0 14.4 - - - +
531A PHE* 3.3 36.6 - - + -
563A GLU 3.8 6.1 - - - +
564A VAL 3.0 7.4 + - - +
566A PRO* 1.3 82.5 - - + +
568A VAL* 1.3 58.3 + - - +
569A LEU 3.8 0.2 + - - -
570A LEU* 3.9 15.7 + - - +
604A ASN* 3.6 32.8 - - - +
605A MET* 3.9 19.3 - - - +
608A ALA* 3.4 32.3 - - + -
609A GLY* 3.7 12.3 - - - +
1001A HEM 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 5.0 14.8 - - + -
564A VAL* 2.8 27.8 + - + +
565A VAL* 3.6 25.1 - - + +
567A LEU* 1.3 69.5 - - - +
569A LEU* 1.3 59.8 - - + +
570A LEU 3.1 2.7 - - - -
571A GLY* 2.8 25.2 + - - +
572A ARG* 4.3 2.1 + - - +
605A MET* 5.1 15.7 - - + -
609A GLY* 5.8 0.4 - - - -
610A VAL* 5.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 4.7 17.7 - - + -
565A VAL* 3.1 23.6 - - + +
566A PRO* 3.2 16.1 + - + +
568A VAL* 1.3 83.4 - - + +
570A LEU* 1.3 65.7 + - + +
571A GLY 3.1 1.1 + - - -
572A ARG* 3.5 12.9 + - + +
573A GLU* 3.5 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A PRO 4.2 12.8 - - - +
567A LEU* 3.9 11.8 + - - +
568A VAL 3.1 0.8 - - - -
569A LEU* 1.3 77.8 - - + +
571A GLY* 1.3 57.2 + - - +
572A ARG 3.3 0.7 - - - -
573A GLU* 3.6 20.2 - - + +
574A ALA* 2.8 31.9 + - - +
600A VAL* 6.2 0.7 - - + -
601A ALA* 3.6 42.0 - - + +
604A ASN* 3.7 25.4 - - + +
605A MET* 4.9 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A VAL* 2.8 18.6 + - - +
570A LEU* 1.3 77.2 - - - +
572A ARG* 1.3 58.1 + - - +
574A ALA* 4.2 3.5 - - - +
575A TYR* 4.1 12.3 + - - +
578A TRP* 5.9 1.2 - - - -
605A MET* 3.5 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A MET* 5.9 9.4 - - - -
251A TYR* 4.1 29.6 + - - -
568A VAL 4.3 2.2 + - - +
569A LEU* 3.5 14.5 + - + +
570A LEU 3.3 0.2 - - - -
571A GLY* 1.3 73.8 - - - +
573A GLU* 1.3 55.6 + - - +
574A ALA 3.2 2.2 - - - -
575A TYR* 3.2 12.8 + - - +
576A GLU* 2.8 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A LEU 3.5 6.4 + - - +
570A LEU* 3.4 32.0 + - + +
572A ARG* 1.3 78.2 - - - +
574A ALA* 1.3 52.3 + - - +
576A GLU* 3.6 10.1 - - + +
577A HIS* 2.8 75.4 + - - -
580A TYR* 5.7 2.3 - - - -
601A ALA* 4.8 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A LEU 2.8 18.2 + - - +
571A GLY* 4.2 7.6 - - - +
573A GLU* 1.3 74.7 - - - +
575A TYR* 1.3 60.1 + - - +
577A HIS* 3.2 10.0 + - - +
578A TRP* 2.8 54.5 + - + +
598A VAL* 5.5 5.2 - - + +
601A ALA* 5.2 10.9 - - + +
602A PHE* 5.3 8.3 - - + +
605A MET* 5.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A GLY 4.1 7.2 + - - +
572A ARG* 3.2 16.1 + - - +
574A ALA* 1.3 74.8 - - - +
576A GLU* 1.3 80.2 + - - +
578A TRP* 3.1 32.1 + + + +
579A SER* 2.8 51.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ARG* 2.8 57.3 + - - +
573A GLU* 3.6 13.9 - - + +
575A TYR* 1.3 94.2 - - - +
577A HIS* 1.3 51.1 + - - +
579A SER* 3.2 5.7 + - - +
580A TYR* 2.8 75.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A GLU* 2.8 56.8 + - - -
574A ALA* 3.3 11.7 - - - +
576A GLU* 1.3 71.9 - - - +
578A TRP* 1.3 55.2 + - - +
580A TYR* 2.8 13.6 + + - +
581A GLN* 2.8 37.6 + - - +
594A LEU* 4.2 30.1 - - + +
597A PHE* 5.4 6.2 + - + +
598A VAL* 3.8 32.1 - - + -
601A ALA* 5.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A GLY 5.9 1.6 - - - -
574A ALA* 2.8 43.3 + - + +
575A TYR* 3.1 35.6 + + + +
577A HIS* 1.3 73.1 - - - +
579A SER* 1.3 57.4 + - - +
580A TYR 3.8 0.3 + - - -
581A GLN* 4.0 22.1 + - - +
582A HIS* 4.0 18.9 + - - -
598A VAL* 4.8 18.6 + - + +
602A PHE* 5.2 15.8 - + + +
605A MET* 6.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A TYR* 2.8 42.2 + - - -
576A GLU* 3.3 7.4 - - - -
578A TRP* 1.3 71.9 - - - +
580A TYR* 1.3 69.9 + - - +
581A GLN 3.9 0.2 - - - -
582A HIS* 5.0 7.4 - - - -
----------------------------------------------------------
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