Contacts of the strand formed by residues 269 - 273 (chain A) in PDB entry 3GEB
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 ARG 269 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A MET* 4.3 9.2 - - - -
268A GLU* 1.3 73.9 - - - +
270A VAL* 1.3 64.5 + - - +
271A PHE* 3.8 22.6 - - + -
438A ARG* 4.4 0.4 - - - +
440A ASN 3.0 4.8 + - - +
441A CYS* 3.3 16.2 - - - -
442A VAL* 3.0 24.4 + - - +
496A VAL* 3.2 29.9 - - + +
498A VAL* 4.5 5.5 - - + +
536A GLU* 2.6 52.9 + - - -
538A LEU* 3.5 20.2 - - + -
269D ARG* 5.8 0.4 - - - +
537D TYR* 2.3 65.4 + - - +
538D LEU* 4.5 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU* 5.5 0.9 - - + -
269A ARG* 1.3 75.9 - - - +
271A PHE* 1.3 63.6 + - - +
272A VAL* 3.8 10.2 + - + +
442A VAL* 3.7 10.8 - - + +
444A VAL* 3.7 28.5 - - + -
487A ILE* 4.5 0.9 - - + -
491A PHE* 3.8 30.3 - - + -
495A ALA* 4.3 10.8 - - + -
496A VAL 3.1 4.9 + - - +
497A TYR* 3.4 36.9 - - + +
498A VAL* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ARG* 3.8 21.8 - - + -
270A VAL* 1.3 73.8 - - - +
272A VAL* 1.3 61.5 + - - +
273A TRP* 3.4 20.1 - - + +
435A ILE* 3.5 28.9 - - + -
441A CYS* 3.7 26.7 - - + -
442A VAL 2.8 14.3 + - - +
444A VAL* 2.8 31.2 + - - +
498A VAL* 3.6 15.5 - - + -
500A ILE* 3.8 20.4 - - + -
529A LEU* 4.5 6.1 - - + -
533A LEU* 3.7 15.0 - - + -
537D TYR* 3.5 42.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 4.1 23.1 - - + +
271A PHE* 1.3 72.7 - - - +
273A TRP* 1.3 61.3 + - - +
444A VAL* 3.6 7.4 - - + -
446A VAL* 3.5 32.1 - - + -
484A PHE* 3.5 22.5 - - + -
487A ILE* 4.1 18.4 - - + -
497A TYR* 4.6 10.5 - - + -
498A VAL 2.9 14.6 + - - +
499A VAL* 3.6 13.2 - - + +
500A ILE* 3.1 24.3 + - - +
515A MET* 6.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 3.4 24.1 - - + +
272A VAL* 1.3 75.6 - - - +
274A ASP* 1.3 66.7 + - - +
278A THR* 3.7 15.5 - - + -
279A ILE* 3.3 34.1 - - + -
428A SER* 4.5 4.3 - - - -
431A ALA* 4.0 13.9 - - + -
432A LEU* 3.4 21.0 - - + +
435A ILE* 3.6 18.4 - - + -
443A ASN* 2.9 22.9 + - - -
444A VAL 2.9 17.7 + - - +
445A LEU* 3.7 3.5 - - + +
446A VAL* 3.0 30.8 + - - +
467A PHE* 4.1 6.5 - + - -
480A LYS* 5.5 0.2 - - - -
500A ILE* 3.6 32.3 - - + -
520A ILE* 4.3 6.3 - - + -
526A LEU* 4.6 8.5 - - + -
529A LEU* 3.8 18.6 - - + -
----------------------------------------------------------
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