Contacts of the strand formed by residues 84 - 89 (chain W) 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 GLY 84 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46W THR* 4.0 6.0 + - - -
79W ASN* 3.7 7.6 - - - +
80W ASN* 2.9 41.5 + - - +
82W GLY 3.4 0.4 - - - -
83W LYS* 1.3 81.1 - - - +
85W LEU* 1.3 64.3 + - - +
291W LEU 3.5 9.6 - - - -
292W VAL* 4.8 6.5 - - - -
303W THR* 4.5 3.8 - - - +
308W LYS* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46W THR* 4.2 11.0 - - - +
49W ILE* 3.4 34.1 - - + -
50W LYS* 3.3 33.2 - - - +
77W TYR* 3.9 16.6 - - + -
78W ALA 3.6 13.2 - - - +
84W GLY* 1.3 75.5 - - - +
86W ILE* 1.3 79.4 + - - +
87W MET* 4.2 13.2 - - + -
106W ILE* 5.9 0.4 - - + -
289W THR 3.9 0.3 - - - +
290W ILE* 3.7 1.5 - - - +
291W LEU* 2.8 57.9 + - + +
292W VAL* 5.6 0.8 - - - +
308W LYS* 5.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76W VAL 4.1 0.2 - - - +
77W TYR* 3.3 3.5 - - - -
78W ALA* 2.9 53.5 + - + +
85W LEU* 1.3 78.9 - - - +
87W MET* 1.3 65.8 + - - +
88W PHE* 3.5 31.8 - - + -
288W ILE* 4.9 3.6 - - + -
289W THR 3.1 11.9 - - - +
290W ILE* 4.3 13.9 - - + -
308W LYS* 3.7 17.5 - - + -
309W PHE* 3.6 40.2 - - + +
312W ASN* 4.5 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53W GLU* 3.2 43.7 - - - +
57W TYR* 4.1 14.1 - - + -
76W VAL 3.5 4.0 - - - -
77W TYR* 4.3 7.4 - - + -
85W LEU* 4.2 22.2 - - + -
86W ILE* 1.3 77.8 - - - +
88W PHE* 1.3 64.5 + - - +
274W PHE* 3.3 25.4 - - + -
277W MET* 3.2 26.6 - - + +
288W ILE* 3.1 9.5 - - - +
289W THR* 2.8 54.0 + - + +
291W LEU* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57W TYR* 3.1 24.3 - - - -
59W ASN* 5.9 1.1 - - - -
75W LYS* 3.5 0.9 - - - -
76W VAL* 2.8 36.5 + - + +
77W TYR* 5.3 1.1 - - - -
78W ALA* 5.3 2.0 - - + -
86W ILE* 3.5 34.5 - - + -
87W MET* 1.3 78.4 - - - +
89W LEU* 1.3 62.4 - - - +
90W ILE* 4.8 7.4 - - + -
95W LEU* 6.0 0.9 - - + -
99W PHE* 4.6 6.1 - + - -
277W MET* 3.9 1.3 - - - -
286W THR* 5.0 5.6 - - + -
287W CYS 3.8 1.1 - - - -
288W ILE* 3.0 31.4 - - + -
312W ASN* 3.5 27.8 - - - -
313W THR* 4.1 25.1 - - + -
316W ASP* 4.0 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57W TYR* 4.8 4.3 - - - +
73W GLY* 4.8 7.2 - - - +
74W ASP 3.4 14.6 - - - +
75W LYS* 4.4 18.8 - - + -
88W PHE* 1.3 79.0 - - - +
90W ILE* 1.3 68.3 + - - +
277W MET* 4.1 10.1 - - + +
280W MET* 3.3 35.9 - - + +
281W LYS* 5.4 1.1 - - - -
282W ASN 6.1 1.1 - - - +
283W ALA* 4.0 18.2 - - + +
286W THR* 3.1 14.6 - - - +
287W CYS* 3.2 42.0 + - - +
----------------------------------------------------------
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