Contacts of the strand formed by residues 100 - 105 (chain R) 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 R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R PHE* 1.3 77.1 - - - +
101R ILE* 1.3 62.4 + - - +
102R LEU* 5.1 3.1 - - - +
285R LYS* 4.5 28.0 - - + +
286R THR 3.3 5.7 + - - -
287R CYS* 3.1 23.0 - - + +
288R ILE 3.0 19.0 + - - +
337R GLU* 2.9 31.2 + - + +
395R ILE* 5.0 8.7 - - - +
462R PHE* 3.5 58.5 + - + +
463R LEU* 4.2 7.9 - - - +
464R ASN 4.0 19.7 + - - -
465R ASN* 5.1 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R PHE* 4.0 14.8 - - + -
100R LYS* 1.3 74.7 - - - +
102R LEU* 1.3 71.5 + - - +
288R ILE* 3.1 26.9 - - + +
290R ILE* 3.4 29.4 - - + -
309R PHE* 3.6 31.0 - - + -
333R LEU* 5.4 1.8 - - + -
336R SER* 4.7 2.2 - - - +
337R GLU 3.0 7.8 + - - +
338R MET* 3.3 21.4 - - + -
339R LEU 3.0 23.6 + - - -
423R LEU* 5.0 0.2 - - + -
428R MET* 3.4 26.5 - - + -
462R PHE* 3.9 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100R LYS 5.1 2.7 - - - +
101R ILE* 1.3 85.2 - - - +
103R GLY* 1.3 59.1 + - - +
273R SER* 3.8 35.9 - - - +
276R ALA* 4.8 3.8 - - + -
277R MET* 4.8 5.4 - - + +
288R ILE 2.8 7.1 + - - +
289R THR* 3.3 16.5 - - - +
290R ILE 2.7 27.9 + - - +
339R LEU* 3.6 30.3 - - + +
459R TYR* 4.1 29.6 - - + +
462R PHE* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R ILE* 4.2 1.8 - - - +
102R LEU* 1.3 75.0 - - - +
104R ALA* 1.3 66.2 + - - +
273R SER* 5.6 2.0 - - - -
290R ILE* 3.5 13.2 - - - -
291R LEU* 5.2 0.2 - - - -
338R MET* 4.6 8.2 - - - +
339R LEU 3.8 9.5 + - - -
340R SER* 4.3 9.3 - - - +
341R SER* 3.0 28.5 + - - -
419R ILE* 5.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R GLY* 1.3 75.3 - - - +
105R HIS* 1.3 60.9 + - - +
266R ASP* 3.3 16.4 - - - +
269R CYS 4.4 0.7 - - - -
270R ALA* 3.8 30.5 - - + +
273R SER* 4.6 2.7 - - - +
290R ILE 3.1 4.9 + - - -
291R LEU* 3.1 32.2 - - + +
292R VAL* 3.2 4.3 + - - +
341R SER* 3.9 10.8 - - - +
419R ILE* 4.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R ALA* 1.3 70.3 - - - +
106R ILE* 1.3 60.6 + - - +
107R ASP* 2.8 44.6 + - - +
265R ASP* 3.1 18.5 + - - -
266R ASP* 2.4 69.5 + - + +
267R ARG 4.2 0.3 + - - -
270R ALA* 4.4 1.0 - - - +
292R VAL* 2.9 15.9 - - + +
295R GLU* 3.0 43.1 + - + -
296R GLU* 3.5 5.2 - - + -
341R SER 4.9 0.4 + - - -
342R ASP* 3.5 7.0 - - + -
419R ILE* 4.7 6.1 - - + +
6036R MN 2.7 23.6 + - - -
----------------------------------------------------------
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