Contacts of the strand formed by residues 434 - 442 (chain A) in PDB entry 1FO4
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 VAL 434 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLN* 3.1 26.1 + - - +
432A ALA* 4.3 1.3 - - - +
433A LYS* 1.3 86.9 - - - +
435A THR* 1.3 64.8 + - - +
456A TYR* 4.1 16.8 - - + -
457A GLY 3.5 10.8 - - - +
459A MET* 3.9 9.2 - - + -
508A ARG* 3.7 39.3 - - + +
511A LEU* 3.9 18.2 - - + -
512A THR* 4.1 10.8 - - + -
515A PHE* 3.5 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLN* 2.9 25.1 + - - -
358A ILE 4.2 2.7 - - - +
359A SER 3.4 24.5 - - - +
360A ASP* 2.8 28.7 + - - +
363A PRO* 4.3 2.6 - - + +
421A PHE 3.4 6.9 + - - -
422A LYS* 4.1 2.3 - - - +
432A ALA* 3.6 11.7 - - + -
434A VAL* 1.3 75.2 - - - +
436A CYS* 1.3 61.6 + - - +
456A TYR* 3.4 1.9 - - - +
457A GLY* 2.6 49.7 + - - +
515A PHE* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLN* 3.6 8.8 + - - -
363A PRO* 4.1 8.3 - - - -
364A VAL* 4.1 0.9 - - - +
420A ALA* 3.4 5.9 - - - +
421A PHE* 3.0 45.0 + - - -
435A THR* 1.3 77.2 + - - +
437A GLY* 1.3 60.7 + - - +
438A MET* 3.8 23.8 - - + -
455A CYS 3.2 13.5 - - - +
456A TYR* 3.5 18.6 - - + -
515A PHE* 3.5 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 3.7 18.7 - - - +
364A VAL* 4.1 9.2 - - - -
367A ALA* 3.3 13.5 - - - +
418A PHE* 4.3 1.1 - - - -
419A SER 3.7 4.9 - - - -
436A CYS* 1.3 74.5 - - - +
438A MET* 1.3 64.2 + - - +
455A CYS 2.9 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A PHE* 3.1 10.3 - - - -
419A SER* 2.7 41.7 + - - +
421A PHE* 4.8 3.6 - - - -
436A CYS* 3.8 18.2 - - + -
437A GLY* 1.3 80.8 - - - +
439A ARG* 1.3 61.0 + - - +
453A ALA 3.5 2.9 - - - -
454A LEU* 3.4 25.4 - - + -
456A TYR* 3.1 42.8 - - + +
515A PHE* 3.8 6.1 - - + +
516A PHE* 3.7 19.1 - - - +
519A PHE* 3.5 43.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A VAL* 5.6 2.5 - - - -
367A ALA 3.1 28.7 + - - +
368A SER* 4.0 14.8 + - - +
413A ARG* 3.1 21.2 - - - +
416A GLU* 2.6 25.9 + - + +
417A PHE 3.4 9.2 - - - +
418A PHE* 3.3 16.6 - - + -
438A MET* 1.3 75.9 - - - +
440A VAL* 1.3 64.4 + - - +
441A LEU* 4.1 5.4 - - - +
451A GLU* 2.4 46.7 + - - +
452A LEU* 3.5 7.2 - - - +
453A ALA* 2.9 47.1 + - - +
519A PHE* 3.9 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASP 3.8 0.9 - - - +
416A GLU* 3.3 6.7 - - - +
417A PHE* 2.9 45.8 + - + +
439A ARG* 1.3 76.9 - - - +
441A LEU* 1.3 66.1 + - - +
442A PHE* 3.7 33.2 - - + -
449A VAL* 4.4 5.2 - - + -
451A GLU 3.4 11.0 - - - +
452A LEU* 4.0 7.0 - - + -
478A TRP* 3.7 23.6 - - + -
519A PHE* 3.7 21.8 - - + -
523A VAL* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ARG* 4.0 24.7 - - + +
414A GLU 4.0 9.2 - - - +
415A ASP* 3.6 3.1 - - + +
416A GLU* 3.9 24.2 - - + -
439A ARG* 4.1 7.2 - - - +
440A VAL* 1.3 73.2 - - - +
442A PHE* 1.3 67.9 + - - +
449A VAL* 3.7 1.9 - - - -
450A LYS* 2.6 52.6 + - + +
451A GLU* 2.7 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASP* 2.9 35.3 + - + +
417A PHE* 3.8 13.5 - + - -
440A VAL* 3.7 16.2 - - + -
441A LEU* 1.3 84.5 - - - +
443A GLN* 1.3 67.7 + - - +
444A PRO* 3.7 1.7 - - - +
446A SER 3.4 17.0 - - - +
447A MET* 3.3 36.3 - - - -
448A GLN 3.3 8.1 - - - -
449A VAL* 3.7 9.0 - - + -
450A LYS* 4.1 6.0 - - - +
478A TRP* 3.5 40.4 - + + -
523A VAL* 3.6 20.2 - - + -
527A LEU* 3.7 17.5 - - + -
----------------------------------------------------------
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