Contacts of the helix formed by residues 574 - 593 (chain A) in PDB entry 4OSI
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 GLY 574 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLY 4.1 7.9 + - - -
572A HIS 3.7 0.2 + - - -
573A ASP* 1.3 74.1 - - - +
575A GLY* 1.3 65.6 + - - +
576A LYS 3.2 2.9 - - - -
577A GLN* 2.9 16.8 + - - +
578A ALA* 3.0 12.8 + - - +
11I T 3.7 33.6 + - - +
12I C 3.7 16.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ALA* 4.7 6.1 - - - +
569A ILE 4.1 11.0 - - - -
570A ALA* 4.0 13.7 - - - -
572A HIS* 3.3 14.2 + - - -
573A ASP 3.1 5.4 - - - -
574A GLY* 1.3 76.4 - - - +
576A LYS* 1.3 63.2 + - - +
578A ALA* 2.9 15.9 + - - +
579A LEU* 2.9 21.0 + - - +
11I T 4.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A GLN* 3.1 49.7 + - + +
544A ALA* 4.2 7.5 - - - +
547A THR* 2.8 34.5 - - - +
550A ARG* 4.6 6.1 - - - +
574A GLY 3.2 0.4 + - - -
575A GLY* 1.3 72.4 - - - +
577A GLN* 1.3 74.9 + - - +
579A LEU* 3.3 3.2 + - - +
580A GLU* 2.9 50.0 + - - +
11I T 4.0 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A GLY 2.9 9.5 + - - +
576A LYS* 1.3 92.6 - - - +
578A ALA* 1.3 58.2 + - - +
580A GLU* 3.1 9.8 + - - +
581A THR* 2.4 35.7 + - - -
610A LYS* 2.9 41.9 + - + +
11I T 3.5 47.9 + - - +
12I C 4.0 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A ILE* 3.6 26.9 - - + +
573A ASP 5.8 0.4 - - - +
574A GLY 3.0 10.3 + - - +
575A GLY* 2.9 15.2 + - - +
577A GLN* 1.3 72.9 - - - +
579A LEU* 1.3 55.6 + - - +
581A THR* 3.6 5.3 + - - -
582A VAL* 2.9 32.2 + - - +
604A ALA* 3.9 13.7 - - + +
606A ASN 5.3 1.1 - - - +
609A GLY* 4.6 4.5 - - - +
610A LYS* 4.0 18.1 - - - +
613A LEU* 4.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ALA 4.5 1.6 - - - +
547A THR* 3.8 31.6 - - + +
548A VAL* 3.6 31.2 - - + -
551A LEU* 4.1 7.6 - - + +
555A LEU* 3.9 24.8 - - + +
566A VAL* 4.3 13.0 - - + +
569A ILE* 3.8 29.2 - - + -
570A ALA* 4.2 8.5 - - + -
575A GLY 2.9 18.0 + - - +
576A LYS 3.5 7.0 - - - +
578A ALA* 1.3 69.8 - - - +
580A GLU* 1.3 65.3 + - - +
582A VAL* 3.2 4.0 + - - +
583A GLN* 2.9 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A THR* 4.1 5.6 - - + -
550A ARG* 3.1 34.5 + - - +
551A LEU* 4.7 1.3 - - - -
576A LYS* 2.9 55.3 + - + +
577A GLN* 3.1 9.4 + - - +
579A LEU* 1.3 72.2 - - - +
581A THR* 1.3 58.0 + - - +
583A GLN* 3.4 15.9 + - - +
584A ARG* 2.9 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLN 2.4 27.2 + - - -
578A ALA 3.6 3.8 - - - -
580A GLU* 1.3 74.2 - - - +
582A VAL* 1.3 68.5 + - - +
584A ARG* 3.9 16.5 + - - +
585A LEU* 2.9 32.5 + - + +
610A LYS* 2.9 43.5 + - + +
613A LEU* 4.1 12.8 - - + -
614A GLU* 3.7 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 4.5 3.8 - - + -
561A LEU* 4.4 11.7 - - + -
569A ILE* 3.9 15.7 - - + -
578A ALA 2.9 27.5 + - - +
579A LEU* 3.2 6.9 + - - +
581A THR* 1.3 74.2 - - - +
583A GLN* 1.3 59.0 + - - +
585A LEU* 2.5 27.4 + - - -
586A LEU* 2.9 46.1 + - + +
600A VAL* 4.6 9.0 - - + +
601A VAL* 5.8 0.9 - - + -
604A ALA* 3.5 28.5 - - + -
613A LEU* 3.9 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ARG* 5.1 1.2 + - - -
551A LEU* 3.3 31.3 - - + +
554A VAL* 4.6 7.7 - - + +
555A LEU* 3.8 17.2 - - + +
559A HIS* 3.5 33.4 + - + -
579A LEU 2.9 16.1 + - - +
580A GLU* 3.6 18.0 - - - +
582A VAL* 1.3 76.8 - - - +
584A ARG* 1.3 66.2 + - - +
587A PRO* 4.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A GLU* 2.9 19.4 + - - +
581A THR* 3.8 21.9 + - - +
582A VAL 2.6 4.0 + - - -
583A GLN* 1.3 82.6 - - - +
585A LEU* 1.3 87.6 + - + +
587A PRO* 3.8 14.2 - - - +
588A VAL* 4.2 3.9 - - + +
610A LYS* 5.0 6.9 - - - +
614A GLU* 3.6 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A THR* 2.9 33.2 + - + +
582A VAL* 2.5 13.6 + - - -
584A ARG* 1.3 99.0 - - + +
586A LEU* 1.3 64.1 + - - +
587A PRO 3.2 3.4 - - - -
588A VAL* 3.2 25.8 + - + -
589A LEU* 2.8 39.3 + - + +
613A LEU* 4.6 6.5 - - + -
614A GLU* 4.4 15.3 - - + +
617A GLN* 4.4 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 5.0 0.4 - - + -
559A HIS* 3.9 25.6 - - + +
561A LEU* 3.6 30.7 - - + -
582A VAL* 2.9 41.8 + - + +
585A LEU* 1.3 68.3 - - - +
587A PRO* 1.4 75.7 - - + +
589A LEU* 4.6 3.3 - - - +
590A CYS* 3.0 49.6 + - - +
597A PRO* 3.9 13.9 - - + -
600A VAL* 3.8 20.8 - - + +
601A VAL* 5.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A HIS* 4.0 15.5 - - + +
583A GLN 4.0 12.3 - - - +
584A ARG 3.8 13.2 - - - +
585A LEU 3.6 1.1 - - - -
586A LEU* 1.4 96.3 - - + +
588A VAL* 1.3 70.2 + - + +
589A LEU 3.0 0.2 + - - -
590A CYS 3.2 0.5 + - - -
591A GLN* 2.1 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A ARG 4.2 7.6 - - - +
585A LEU* 3.2 32.5 + - + +
587A PRO* 1.3 75.4 - - + +
589A LEU* 1.3 61.7 + - - +
591A GLN* 3.4 9.0 + - - +
592A ALA* 3.5 8.8 + - + -
593A HIS* 2.9 29.2 + - + -
617A GLN* 5.0 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A LEU* 2.8 32.9 + - + +
586A LEU 3.9 2.2 - - - +
588A VAL* 1.3 72.1 - - - +
590A CYS* 1.3 60.5 + - - +
591A GLN 2.9 6.8 + - - -
593A HIS* 3.1 33.5 - - + +
595A LEU* 3.5 25.8 + - + -
600A VAL* 3.6 27.8 - - + -
603A ILE* 5.0 1.3 - - + -
613A LEU* 3.5 34.3 - - + +
616A VAL* 4.3 3.8 - - + -
617A GLN* 4.1 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LEU* 3.0 33.3 + - - +
589A LEU* 1.3 76.7 - - - +
591A GLN* 1.3 79.5 + - - +
594A GLY* 4.2 7.0 - - - -
595A LEU 2.7 32.4 - - - +
596A THR 3.5 3.4 - - - -
597A PRO* 3.3 34.3 - - - -
600A VAL* 4.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LEU 3.8 0.2 + - - -
587A PRO* 2.1 47.7 + - - +
588A VAL* 3.8 5.2 - - - +
589A LEU 2.9 3.8 + - - -
590A CYS* 1.3 105.3 - - - +
592A ALA* 1.3 57.1 + - + +
593A HIS 2.6 16.0 + - - -
594A GLY* 2.9 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A VAL* 3.5 7.2 + - + +
591A GLN* 1.3 76.0 - - + +
593A HIS* 1.3 83.2 + - + +
621A PRO* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A VAL* 2.9 41.1 + - + -
589A LEU* 3.1 20.4 + - + +
591A GLN 2.6 7.7 + - - -
592A ALA* 1.3 94.7 + - + +
594A GLY* 1.3 57.9 + - - +
595A LEU* 3.0 24.0 + - + +
617A GLN* 4.0 27.5 + - + -
620A LEU* 4.2 20.6 - - + +
621A PRO* 4.1 27.4 - - + +
631A PRO* 4.6 14.2 - - - +
----------------------------------------------------------
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