Contacts of the strand formed by residues 575 - 579 (chain A) in PDB entry 4GT5
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 PHE 575 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A VAL* 5.2 1.6 - - + -
503A HIS 5.5 0.2 - - - -
561A ALA* 3.7 13.7 - - + -
564A LEU* 3.9 26.0 - - + +
565A THR* 3.2 27.1 - - - -
568A GLN* 3.3 27.4 + - - +
573A VAL 3.5 4.2 + - - +
574A ARG* 1.3 80.8 + - - +
576A PHE* 1.3 61.8 + - - +
577A GLY* 3.3 42.2 - - - -
578A VAL* 3.7 13.5 - - + -
587A MET* 3.4 22.7 - - + -
588A VAL 3.6 11.2 - - - -
589A PHE* 3.8 22.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A HIS* 3.3 25.3 + - - +
505A ILE* 4.6 4.2 - - + +
532A LEU* 4.0 28.9 - - + +
533A LEU* 4.3 13.0 - - + -
539A MET* 4.0 25.1 - - + -
541A VAL* 4.3 2.9 - - + -
574A ARG* 3.4 49.1 - - - -
575A PHE* 1.3 76.7 - - - +
577A GLY* 1.3 58.2 + - - +
588A VAL* 2.9 24.1 + - + +
589A PHE 3.8 17.0 - - - -
590A GLU* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A HIS* 3.3 18.8 - - - -
505A ILE* 4.6 3.6 - - - -
575A PHE* 3.3 21.5 - - - -
576A PHE* 1.3 81.5 - - - +
578A VAL* 1.3 64.6 + - - +
588A VAL* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A VAL* 4.7 7.0 - - + -
503A HIS 2.9 16.9 + - - +
504A HIS* 3.4 31.4 - - + +
505A ILE* 2.8 31.5 + - - +
557A PHE* 3.8 20.6 - - + -
558A GLN* 5.5 3.4 - - - +
561A ALA* 3.8 20.0 - - + -
575A PHE* 3.7 17.3 - - + -
577A GLY* 1.3 78.6 - - - +
579A CYS* 1.3 59.2 + - - +
580A THR* 4.6 8.1 - - + -
586A LEU 3.4 8.5 - - - +
587A MET* 4.0 6.1 - - + -
588A VAL* 4.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A HIS* 5.4 0.9 - - - -
505A ILE 3.4 21.1 - - - +
507A ARG* 3.8 40.2 - - - -
510A ILE* 4.2 9.4 - - + -
578A VAL* 1.3 74.5 - - - +
580A THR* 1.3 67.6 + - - +
581A GLU* 3.9 13.2 - - - -
582A GLY 5.4 0.9 - - - -
584A PRO 4.4 2.0 - - - +
585A LEU* 3.6 2.8 - - - -
586A LEU* 3.0 51.3 + - + +
----------------------------------------------------------
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