Contacts of the strand formed by residues 431 - 441 (chain A) in PDB entry 1IVV
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 HIS 431 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A VAL* 4.1 4.7 - - + -
283A PRO 3.1 17.5 - - - +
284A TYR* 3.7 27.0 - + + -
382A DAH 3.1 11.6 + - - -
406A VAL* 5.4 1.3 - - + -
407A PHE 5.8 2.2 - - - -
429A PRO 3.0 18.7 + - - -
430A PHE* 1.3 75.3 - - - +
432A GLN* 1.3 62.1 + - - +
433A HIS* 2.9 19.7 + + - -
592A HIS* 2.7 60.2 + + + +
594A PRO* 3.7 13.0 - - + -
1001A CU 1.9 33.0 - - - -
470B PHE* 3.5 7.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A VAL* 3.1 31.2 - - - +
283A PRO* 3.0 14.3 + - + +
431A HIS* 1.3 79.6 - - - +
433A HIS* 1.3 63.7 + - - +
434A ILE* 3.7 22.9 - - + +
520A PRO 4.1 1.8 + - - -
521A THR 3.0 23.8 + - - -
522A LEU* 3.7 11.3 - - - +
523A LEU* 3.0 35.3 + - - +
524A ALA 4.7 0.5 + - - -
590A LEU 3.2 9.9 - - - +
591A THR* 3.1 24.8 + - - +
470B PHE* 3.8 16.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A MET* 5.0 1.3 - - + -
281A VAL 3.5 5.2 - - - -
282A VAL* 3.8 9.1 - - + +
382A DAH 3.2 30.5 - + - -
384A TYR* 3.0 30.2 + + + -
402A ALA* 5.1 7.4 - - + +
431A HIS* 2.9 13.5 + + - -
432A GLN* 1.3 71.4 - - - +
434A ILE* 1.3 59.3 + - - +
435A PHE* 3.5 21.9 - - + -
589A GLY* 2.9 3.6 - - - -
590A LEU* 2.8 55.4 + - + +
592A HIS* 4.3 4.3 - - + -
602A MET* 5.7 1.9 - - + +
1001A CU 2.0 32.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A MET* 3.2 3.2 - - - +
281A VAL* 2.8 50.7 + - + +
432A GLN* 3.7 41.3 - - + +
433A HIS* 1.3 76.8 - - - +
435A PHE* 1.3 64.8 + - - +
520A PRO 4.8 1.1 - - - +
521A THR* 4.0 4.3 - - - -
522A LEU* 3.8 33.4 - - + +
536A PHE* 4.1 3.0 - - + -
537A ALA* 3.8 11.2 - - + -
587A THR* 3.6 30.1 - - + -
588A PHE 3.8 8.5 - - - +
589A GLY* 4.4 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 4.3 13.7 - - + -
279A GLU 3.6 5.4 - - - +
280A MET* 3.6 42.2 - - + -
384A TYR* 4.8 8.1 - + - -
386A PHE* 4.5 9.4 - + - -
398A PHE* 4.9 1.8 - + - -
400A ALA* 3.5 27.8 - - + -
401A LYS 6.3 0.2 - - - -
402A ALA* 5.7 3.8 - - + -
433A HIS* 3.5 26.7 - - + -
434A ILE* 1.3 79.7 - - - +
436A SER* 1.3 62.5 + - - +
536A PHE* 3.9 1.9 - - - -
587A THR* 3.4 5.2 - - - -
588A PHE* 2.8 68.2 + + + +
589A GLY* 4.2 0.9 - - - -
590A LEU* 5.5 0.7 - - + -
607A VAL* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 3.2 8.3 - - - -
278A ALA* 2.9 26.6 + - - +
279A GLU 3.0 11.2 + - - -
435A PHE* 1.3 74.6 - - - +
437A ALA* 1.3 61.6 + - - +
536A PHE* 3.4 28.9 - - - +
553A PRO* 3.6 26.8 - - - +
567A LEU* 5.0 0.2 - - - +
585A TRP* 4.5 13.0 - - - +
586A HIS 3.4 7.5 + - - -
587A THR* 4.7 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER 3.2 8.5 - - - +
277A ILE* 4.0 7.6 - - + -
388A TRP* 4.9 1.1 - - + -
436A SER* 1.3 74.3 - - - +
438A ARG* 1.3 59.5 + - - +
439A LEU* 3.9 9.3 - - + +
584A VAL 3.4 2.4 - - - +
585A TRP* 3.3 5.4 - - - -
586A HIS* 3.0 36.3 + - + +
588A PHE* 4.0 6.4 - - + -
609A PHE* 3.5 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 3.4 39.3 + - - +
275A ALA* 3.6 0.9 - - - -
276A SER* 2.6 40.4 + - - +
278A ALA* 3.7 18.4 - - + -
436A SER 3.8 1.2 + - - -
437A ALA* 1.3 71.7 - - - +
439A LEU* 1.3 62.3 + - - +
440A ASP* 3.9 15.2 + - - +
546A TYR* 3.9 22.0 - - - -
547A ALA 4.7 1.2 + - - +
550A GLU 3.6 15.8 + - - -
551A ARG* 3.4 25.5 + - - +
583A VAL* 3.6 35.9 - - + +
584A VAL 3.6 2.2 - - - -
585A TRP* 3.5 28.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 4.4 12.1 - - + -
274A ARG 3.5 2.2 - - - -
275A ALA* 3.9 22.7 - - + -
388A TRP* 4.2 15.9 - - + -
437A ALA* 4.4 11.7 - - + +
438A ARG* 1.3 81.0 - - - +
440A ASP* 1.3 62.3 + - - +
441A MET* 3.0 22.8 + - - +
514A LEU* 4.3 16.2 - - + -
583A VAL* 4.1 1.6 - - - -
584A VAL* 2.7 49.2 + - + +
586A HIS* 5.2 2.2 - - + -
609A PHE* 4.1 22.0 - - + -
611A LEU* 4.2 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 2.9 26.6 + - - -
272A ILE* 3.4 2.9 - - - +
273A ASN* 2.6 60.3 + - - +
274A ARG* 2.8 31.2 + - + +
438A ARG* 3.9 14.8 + - - +
439A LEU* 1.3 70.2 - - - +
441A MET* 1.3 54.4 + - - +
546A TYR* 4.1 11.3 - - - -
581A ASP* 3.8 4.2 - - - +
582A ILE 3.5 13.2 - - - +
583A VAL* 3.8 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ILE* 3.6 9.9 - - + +
272A ILE* 3.5 28.7 - - + -
439A LEU* 3.0 34.6 + - - +
440A ASP* 1.3 74.0 - - - +
442A ALA* 1.3 59.4 + - - +
443A ILE* 3.7 16.6 - - + -
446A PHE* 3.7 15.9 - - - -
448A ASN* 3.4 20.1 + - - +
497A ILE* 3.7 36.8 - - + -
581A ASP* 4.5 0.5 - - - +
582A ILE* 3.2 25.3 + - + +
584A VAL* 3.9 16.8 - - + -
611A LEU* 4.7 3.8 - - + -
----------------------------------------------------------
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