Contacts of the strand formed by residues 445 - 448 (chain S) in PDB entry 2GLJ
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 GLU 445 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260S MET* 3.2 5.7 - - - -
261S GLY 2.9 29.5 + - - +
263S GLY* 3.3 10.4 + - - -
264S GLN* 2.8 48.3 + - + +
265S ASP* 3.0 26.1 + - - +
437S LEU* 4.0 7.1 - - + +
438S LEU 3.7 4.3 - - - +
439S ASN* 3.5 19.7 - - - +
440S MSE 3.7 5.4 - - - -
441S HIS* 3.0 23.6 + - - -
442S ALA 3.5 15.5 - - - +
444S TRP* 1.3 73.5 - - - +
446S ILE* 1.3 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 446 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252S TYR* 3.6 37.5 - - + +
258S MET* 3.6 39.7 - - + -
259S VAL 3.2 4.5 - - - +
260S MET* 4.0 21.1 - - + -
363S LEU* 5.1 2.1 - - + +
437S LEU* 3.1 18.6 - - - +
438S LEU* 3.1 47.9 + - + +
439S ASN* 4.4 11.0 - - - +
445S GLU* 1.3 80.5 - - - +
447S SER* 1.3 64.9 + - - +
173V GLY 6.1 0.7 - - - -
174V VAL 6.5 0.4 - - - -
175V SER* 5.9 2.2 - - - -
200V ASN* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 447 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S ASN* 5.1 0.2 + - - -
258S MET* 3.0 9.3 - - - -
259S VAL* 2.8 36.9 + - - +
264S GLN* 2.8 30.7 + - - -
268S ILE* 3.7 16.5 - - - +
363S LEU* 4.3 4.3 - - - -
435S VAL* 4.9 1.3 - - - -
436S ALA 4.4 5.2 - - - -
437S LEU* 3.5 11.9 - - - -
446S ILE* 1.3 79.2 - - - +
448S SER* 1.3 61.2 + - - +
449S LYS 3.7 0.2 + - - -
452S ILE* 3.9 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 448 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S TRP* 4.2 6.2 + - - -
257S SER 3.8 8.2 + - - -
258S MET* 4.3 0.9 - - - -
363S LEU* 3.4 22.1 - - - +
364S GLY* 3.8 7.8 - - - -
435S VAL* 5.1 0.2 - - - +
436S ALA 4.7 2.4 + - - -
447S SER* 1.3 72.3 - - - +
449S LYS* 1.3 66.1 + - - +
450S ALA* 3.4 16.5 + - - +
451S ASP* 2.8 44.1 + - - +
452S ILE* 2.8 15.3 + - - +
203V ILE* 4.5 3.2 - - - +
----------------------------------------------------------
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