Contacts of the strand formed by residues 100 - 105 (chain O) 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 LYS 100 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O PHE* 1.3 77.5 - - - +
101O ILE* 1.3 62.1 + - - +
102O LEU* 4.1 3.1 + - - +
285O LYS* 4.5 27.8 - - + +
286O THR 3.3 5.9 + - - -
287O CYS* 3.1 21.2 - - + +
288O ILE 3.0 20.3 + - - +
337O GLU* 2.9 22.7 + - + +
462O PHE* 3.6 50.1 + - + +
463O LEU* 4.3 12.6 - - - +
464O ASN 5.2 0.2 - - - -
465O ASN* 2.7 45.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O PHE* 4.0 14.4 - - + -
100O LYS* 1.3 74.8 - - - +
102O LEU* 1.3 74.8 + - - +
288O ILE* 3.2 28.0 - - + +
290O ILE* 3.4 28.7 - - + -
309O PHE* 3.6 31.0 - - + -
333O LEU* 5.4 2.0 - - + -
336O SER* 4.7 2.0 - - - -
337O GLU 3.0 7.5 + - - +
338O MET* 3.3 19.6 - - + -
339O LEU 3.0 23.2 + - - -
423O LEU* 5.0 0.2 - - + -
428O MET* 3.4 26.7 - - + -
462O PHE* 4.0 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O LYS 5.1 3.1 - - - +
101O ILE* 1.3 84.8 - - - +
103O GLY* 1.3 58.9 + - - +
273O SER* 3.9 35.9 - - - +
276O ALA* 4.8 3.6 - - + -
277O MET* 4.8 5.8 - - + +
288O ILE 2.9 6.7 + - - +
289O THR* 3.4 15.9 - - - +
290O ILE 2.8 27.4 + - - +
339O LEU* 3.5 35.2 - - + +
459O TYR* 4.1 29.6 - - + +
462O PHE* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101O ILE* 4.2 1.6 - - - +
102O LEU* 1.3 75.4 - - - +
104O ALA* 1.3 65.7 + - - +
273O SER* 5.6 1.8 - - - -
290O ILE* 3.5 13.7 - - - -
291O LEU* 5.2 0.2 - - - -
338O MET* 4.6 8.1 - - - +
339O LEU 3.8 7.9 + - - +
340O SER* 4.2 12.0 - - - +
341O SER* 3.0 28.4 + - - -
419O ILE* 5.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O GLY* 1.3 76.0 - - - +
105O HIS* 1.3 60.7 + - - +
266O ASP* 3.3 15.9 - - - +
269O CYS 4.5 0.7 - - - -
270O ALA* 3.8 31.9 - - + +
273O SER* 4.6 2.7 - - - +
290O ILE* 3.1 5.1 + - - +
291O LEU* 3.1 32.3 - - + +
292O VAL* 3.2 4.0 + - - +
341O SER* 3.9 9.4 - - - +
419O ILE* 4.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O ALA* 1.3 70.5 - - - +
106O ILE* 1.3 60.6 + - - +
107O ASP* 2.8 43.2 + - - +
265O ASP* 3.2 13.5 - - - -
266O ASP* 2.4 71.2 + - + +
267O ARG 4.2 0.2 + - - -
270O ALA* 4.4 0.9 - - - +
292O VAL* 2.9 15.3 - - + +
295O GLU* 3.0 37.4 + - + -
296O GLU* 3.6 4.7 - - + -
341O SER 5.4 0.4 - - - -
342O ASP* 3.6 5.4 - - + -
419O ILE* 4.7 7.0 - - + +
6030O MN 2.3 34.6 + - - -
----------------------------------------------------------
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