Contacts of the strand formed by residues 574 - 578 (chain I) in PDB entry 5G04
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 574 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207I ALA* 5.2 0.2 - - - -
571I LYS 3.7 13.9 - - - +
572I PHE* 4.0 2.3 - - + -
573I PRO* 1.3 75.5 - - - +
575I LEU* 1.3 73.7 - - - +
576I TRP* 3.3 50.7 - + + -
585I TYR 3.8 0.7 - - - +
586I LEU* 3.5 6.4 - - - +
587I LEU* 2.9 36.8 + - + +
641I ALA 4.1 15.3 - - - +
642I GLN* 4.1 30.1 - - + -
643I PHE* 3.8 23.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 575 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I HIS* 5.4 5.2 - - - -
207I ALA* 3.3 42.5 - - + +
208I LEU 4.7 8.7 - - - +
209I CYS* 4.1 23.4 - - + -
218I SER* 3.8 24.7 - - - +
219I VAL 4.2 0.9 - - - +
220I VAL* 3.8 11.9 - - + +
233I TYR* 4.2 13.2 - - + -
573I PRO 4.2 0.8 + - - -
574I PHE* 1.3 91.2 - - - +
576I TRP* 1.3 59.5 + - - +
584I HIS* 5.0 2.9 - - + +
585I TYR 3.4 17.0 - - - +
586I LEU* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 576 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209I CYS* 4.1 5.4 - - - -
574I PHE* 3.3 35.0 - + + -
575I LEU* 1.3 72.0 - - - +
577I ASN* 1.3 81.6 + - - +
578I ASN* 3.7 4.1 - - + +
584I HIS 3.5 0.3 - - - -
585I TYR* 2.5 47.4 + + - +
643I PHE* 3.4 60.0 - + + -
644I TYR 4.2 14.8 - - - -
645I ASP* 4.3 13.9 - - - -
646I ASP* 3.7 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 577 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209I CYS* 3.5 22.2 - - - -
210I LEU 4.2 3.5 - - - +
211I SER* 3.4 6.9 - - - -
212I SER* 3.4 28.9 + - - -
576I TRP* 1.3 90.7 + - - +
578I ASN* 1.3 76.8 + - - +
579I LYS* 3.6 12.6 + - - +
582I ASN* 4.1 4.3 + - - +
583I LEU 2.5 36.1 + - - +
584I HIS* 3.7 11.7 - - - +
605I THR* 5.1 1.0 - - - -
646I ASP* 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 578 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576I TRP* 3.7 6.5 + - + +
577I ASN* 1.3 73.9 + - - +
579I LYS* 1.3 51.7 + - - +
580I THR* 2.4 27.5 + - - -
581I SER* 3.0 26.3 + - - +
582I ASN* 2.7 36.4 + - - -
583I LEU 2.9 11.9 + - - +
585I TYR* 4.3 13.4 - - + -
646I ASP* 2.5 52.7 + - + +
647I GLU* 5.6 2.0 - - - +
----------------------------------------------------------
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