Contacts of the strand formed by residues 602 - 613 (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 MET 602 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A DAH 3.0 25.8 - - - +
402A ALA* 3.2 33.7 - - + +
403A THR* 2.7 38.7 - - - +
404A GLY 3.0 15.2 + - - +
405A VAL* 4.9 0.4 - - - +
406A VAL* 4.2 7.4 - - + -
433A HIS* 5.7 2.2 - - + +
590A LEU* 5.7 1.3 - - + -
592A HIS* 4.2 24.0 - - + +
598A ASP* 2.9 31.2 + - - +
601A ILE* 1.3 71.2 - - - +
603A PRO* 1.4 63.7 - - - +
605A ASP* 3.8 23.6 - - + +
353B ALA* 3.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A ARG* 3.2 26.7 - - - +
597A GLU* 3.4 22.4 - - + +
598A ASP* 3.6 9.5 - - - +
601A ILE 3.6 3.3 - - - +
602A MET* 1.4 98.4 - - - +
604A VAL* 1.3 67.3 + - - +
605A ASP* 3.5 1.6 + - - +
352B LEU* 3.4 18.2 - - + +
353B ALA* 4.5 3.4 - - + -
393B ASP* 4.1 26.5 - - + +
612B ARG* 5.1 1.2 + - - -
620B SER* 5.2 1.1 - - - +
621B PRO* 6.4 0.9 - - + -
622B VAL* 4.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PHE* 5.4 0.7 - - + -
401A LYS* 3.8 27.8 - - + -
402A ALA 3.4 5.6 - - - +
403A THR* 3.5 23.3 - - + +
602A MET 3.7 0.8 + - - -
603A PRO* 1.3 76.3 - - - +
605A ASP* 1.3 70.4 + - - +
606A THR* 3.8 11.7 - - + -
351B ILE* 3.3 35.0 - - + +
352B LEU* 2.7 19.4 + - - +
368B ASN* 6.1 1.6 - - - +
393B ASP* 5.1 3.3 - - - +
612B ARG* 4.4 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ALA 3.8 0.2 - - - +
401A LYS* 3.5 0.2 - - - -
402A ALA* 2.9 31.3 + - - +
590A LEU* 3.6 29.7 - - + +
592A HIS* 5.9 2.8 - - - -
602A MET* 3.8 21.2 - - + +
603A PRO 4.6 0.4 - - - +
604A VAL* 1.3 74.1 - - - +
606A THR* 1.3 75.6 + - - +
610B LYS* 4.8 11.1 + - - -
612B ARG* 4.2 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLU* 3.3 28.0 + - - +
400A ALA 3.2 8.1 - - - -
401A LYS* 3.7 25.1 - - + -
517A HIS* 5.4 1.4 + - - -
519A GLN* 5.5 1.7 + - - -
590A LEU* 3.4 16.8 - - - +
604A VAL* 3.8 9.6 - - + -
605A ASP* 1.3 88.7 + - - +
607A VAL* 1.3 63.6 + - - +
610B LYS* 5.2 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLU* 3.6 6.2 - - - +
400A ALA* 3.0 32.1 + - + +
435A PHE* 3.8 26.7 - - + -
517A HIS* 4.0 13.7 - - + +
519A GLN* 3.9 17.7 - - + +
588A PHE* 4.0 9.6 - - + -
589A GLY* 3.5 31.2 - - - +
590A LEU* 3.3 34.8 - - + +
606A THR* 1.3 71.3 - - - +
608A GLY* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A PHE 3.2 14.1 - - - -
399A GLU* 4.5 0.4 - - - -
517A HIS* 3.3 32.9 + - - +
588A PHE* 3.7 24.8 - - - +
607A VAL* 1.3 79.7 - - - +
609A PHE* 1.3 67.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A TRP* 4.0 15.0 - + - -
396A ILE 5.4 0.4 - - - -
397A GLU* 3.3 4.9 + - - +
398A PHE* 3.0 54.9 + + + +
437A ALA* 3.5 31.0 - - + -
439A LEU* 4.1 11.0 - - + -
514A LEU* 4.4 8.1 - - + -
515A HIS 3.5 15.5 - - - +
516A ALA* 4.5 0.2 - - - -
517A HIS* 3.7 8.7 + - - -
586A HIS* 3.6 23.6 - + + +
588A PHE* 3.6 28.0 - + - -
608A GLY* 1.3 75.1 - - - +
610A LYS* 1.3 70.9 + - - +
611A LEU* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TYR* 6.2 0.2 - - + -
395A THR* 4.2 16.8 - - + -
396A ILE 3.1 14.8 - - - +
397A GLU* 3.8 21.9 + - + +
513A LYS 3.7 0.3 - - - +
514A LEU* 3.5 3.1 - - - +
515A HIS* 2.8 49.5 + - + +
609A PHE* 1.3 84.3 - - - +
611A LEU* 1.3 66.2 + - - +
612A ARG* 4.2 20.9 - - + +
605B ASP* 5.2 7.2 + - - -
606B THR* 5.2 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 4.6 13.7 - - + -
395A THR* 3.4 5.0 - - - +
396A ILE* 2.7 47.4 + - + +
439A LEU* 4.2 14.6 - - + -
441A MET* 4.7 10.1 - - + -
497A ILE* 3.6 31.0 - - + -
512A TYR* 3.9 20.9 - - + -
513A LYS 3.1 6.5 - - - +
514A LEU* 4.0 20.4 - - + +
609A PHE* 3.7 25.8 - - + -
610A LYS* 1.3 81.0 - - - +
612A ARG* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ASP* 4.6 7.7 + - - -
395A THR* 3.9 20.8 + - + +
512A TYR* 3.2 4.0 - - - -
513A LYS* 2.6 37.9 + - + +
515A HIS* 3.4 34.2 - - + +
610A LYS* 4.2 16.3 - - - +
611A LEU* 1.3 79.0 - - - +
613A PRO* 1.3 74.9 - - + +
595B ARG* 3.4 43.5 - - - +
598B ASP* 5.0 1.4 + - - -
603B PRO* 4.7 4.4 + - - +
604B VAL 4.3 9.7 + - - -
605B ASP* 4.1 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ASP* 3.5 20.2 - - - +
394A GLY 3.4 24.0 - - - +
395A THR* 4.2 2.9 - - - +
511A GLY 3.8 6.7 - - - +
512A TYR* 3.5 12.8 - - + +
513A LYS* 5.5 0.3 - - - +
612A ARG* 1.3 87.6 - - + +
614A GLU* 1.3 58.9 + - - +
615A GLY 3.9 1.1 - - - -
616A PHE* 3.9 3.4 - - + -
617A PHE* 3.7 20.6 - - + -
595B ARG* 2.9 37.8 + - - +
597B GLU* 3.5 21.5 - - + +
----------------------------------------------------------
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