Contacts of the helix formed by residues 588 - 600 (chain A) in PDB entry 6BGH
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 PRO 588 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ARG 3.7 4.7 - - - +
587A LEU* 1.4 92.3 - - + +
589A GLY* 1.3 60.3 + - - +
590A GLU* 4.1 14.6 - - + +
591A LYS* 2.9 40.9 + - + +
592A LEU* 2.9 15.2 + - - +
1599B LEU* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PRO* 1.3 73.2 - - - +
590A GLU* 1.3 60.9 + - - +
592A LEU* 3.3 32.4 - - - +
593A GLY* 3.5 6.2 + - - -
1599B LEU* 5.6 0.2 - - - +
1601B ARG* 3.7 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PRO* 4.1 13.0 - - + +
589A GLY* 1.3 75.5 - - - +
591A LYS* 1.3 97.4 + - + +
593A GLY* 3.7 1.2 + - - -
594A ARG* 3.1 49.7 + - - +
642A ARG* 2.7 30.8 + - - -
1601B ARG* 4.6 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A LEU* 3.8 22.7 - - + -
588A PRO* 2.9 29.1 + - + +
590A GLU* 1.3 108.6 + - + +
592A LEU* 1.4 55.1 + - - +
594A ARG* 3.1 13.3 + - - +
595A VAL* 2.8 36.4 + - - +
632A TYR* 3.1 24.4 + - + +
636A CYS* 3.9 20.1 - - - +
639A LYS 5.5 6.8 + - - -
640A LYS* 5.9 3.7 - - - +
642A ARG* 4.3 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A ILE* 3.8 11.4 - - + +
587A LEU* 4.7 1.3 - - - +
588A PRO 2.9 8.3 + - - +
589A GLY* 3.3 32.1 - - - +
591A LYS* 1.4 74.9 - - - +
593A GLY* 1.3 65.6 + - - +
595A VAL* 3.3 9.3 - - - +
596A VAL* 3.0 35.0 + - + +
614A ILE* 3.5 29.8 - - + +
1599B LEU* 3.2 45.1 - - + -
1601B ARG* 4.3 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A GLY 3.5 7.1 + - - -
590A GLU 4.2 2.2 - - - -
591A LYS 3.2 0.4 - - - -
592A LEU* 1.3 90.8 - - - +
594A ARG* 1.3 60.7 + - - +
596A VAL* 3.2 9.6 - - - +
597A HIS* 3.0 31.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A GLU* 3.1 38.4 + - - +
591A LYS* 3.1 17.7 + - - +
593A GLY* 1.3 75.5 - - - +
595A VAL* 1.3 65.5 + - - +
597A HIS* 3.1 12.2 + - - +
598A ILE* 3.0 27.2 + - + +
632A TYR* 4.4 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A ILE* 3.5 27.1 - - + -
587A LEU* 4.8 0.4 - - + -
591A LYS 2.8 20.2 + - - +
592A LEU* 3.3 7.4 - - - +
594A ARG* 1.3 74.5 - - - +
596A VAL* 1.3 70.1 + - - +
598A ILE* 2.9 5.0 + - - +
599A ILE* 2.8 39.0 + - + +
616A ILE* 6.3 0.2 - - + -
629A LEU* 3.4 29.6 - - + -
632A TYR* 3.4 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A LEU* 3.0 18.4 + - + +
593A GLY* 3.2 19.3 - - - +
595A VAL* 1.3 78.3 - - + +
597A HIS* 1.3 67.2 + - + +
599A ILE* 4.5 5.4 - - + -
600A GLN* 2.8 59.4 + - + +
607A ARG* 3.3 28.9 - - + +
614A ILE* 4.0 25.4 - - + -
616A ILE* 4.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A GLY* 3.0 23.1 - - - +
594A ARG* 3.1 10.4 + - - +
595A VAL 3.0 1.0 - - - -
596A VAL* 1.3 93.2 - - + +
598A ILE* 1.3 60.3 + - + +
600A GLN* 3.8 3.9 - - - +
601A SER* 3.0 28.8 + - - -
607A ARG* 4.6 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A ARG* 3.0 34.9 + - + +
595A VAL* 2.9 9.9 + - - +
597A HIS* 1.3 78.6 - - + +
599A ILE* 1.3 70.7 + - + +
601A SER* 3.3 18.3 + - - -
602A ARG* 4.0 8.3 - - - +
628A GLU* 3.9 29.1 - - + +
632A TYR* 5.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL* 2.8 43.7 + - + +
596A VAL* 4.0 5.4 - - - +
598A ILE* 1.3 82.4 - - + +
600A GLN* 1.3 62.7 + - + +
601A SER 3.1 4.0 + - - -
602A ARG* 3.2 22.0 + - - +
603A GLU 3.9 0.3 + - - -
616A ILE* 6.3 2.7 - - + -
618A PHE* 3.8 29.8 - - + -
621A LEU* 4.9 2.7 - - + -
625A THR* 3.7 25.2 - - + +
628A GLU* 3.6 26.0 - - + +
629A LEU* 3.6 24.2 - - + +
632A TYR* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A VAL* 2.8 28.9 + - + +
597A HIS* 3.8 3.7 - - - +
599A ILE* 1.3 76.9 - - + +
601A SER* 1.3 59.9 + - - +
602A ARG 3.0 5.8 - - - -
603A GLU* 3.1 17.8 - - - +
606A LEU* 3.1 51.0 - - + +
607A ARG* 2.9 63.6 + - - +
611A PRO* 5.9 0.2 - - - +
616A ILE* 5.4 2.8 - - - +
621A LEU* 6.3 0.9 - - + -
----------------------------------------------------------
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