Contacts of the helix formed by residues 68 - 77 (chain M) in PDB entry 3EXG
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 GLN 68 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M CYS* 3.2 38.7 + - + +
67M GLY* 1.3 84.7 - - - +
69M GLU* 1.3 50.7 + - - +
70M ALA* 3.0 7.0 - - - -
71M CYS* 2.7 34.7 + - + +
72M CYS* 3.8 4.3 + - - -
90M ARG* 3.6 19.5 - - - +
194M GLU* 3.5 28.3 - - - +
196M ASN* 4.5 5.8 + - - +
227M GLY 5.0 1.1 - - - -
257M THR* 3.4 33.2 - - + +
258M TYR 4.0 7.2 - - - +
259M ARG* 3.7 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M MET* 3.7 33.7 - - + +
42M VAL* 3.3 33.6 - - + +
43M ARG* 2.6 51.6 + - - -
65M CYS* 3.9 1.5 - - - +
66M ASP* 3.1 9.5 - - - +
67M GLY 3.1 15.8 + - - -
68M GLN* 1.3 72.5 + - - +
70M ALA* 1.3 60.6 + - - +
72M CYS* 3.6 6.7 + - - -
73M VAL* 3.1 30.7 + - + +
287M PRO* 3.5 7.3 - - + +
288M ILE* 4.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M MET* 4.0 11.5 - - - -
68M GLN 2.9 0.4 + - - -
69M GLU* 1.3 79.6 - - - +
71M CYS* 1.3 55.8 + - - +
74M GLY* 3.0 25.3 + - - +
227M GLY 3.1 25.1 - - - +
228M MET 3.6 23.8 - - - +
229M ASP 4.2 0.4 - - - -
230M ILE* 3.7 15.1 - - + +
233M VAL* 3.6 9.7 - - - +
287M PRO* 3.6 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M GLN* 2.7 22.1 + - + +
70M ALA* 1.3 69.7 - - - +
72M CYS* 1.3 61.1 + - - +
75M LEU* 2.7 37.7 + - - +
94M PHE* 4.8 2.7 - - + -
194M GLU* 4.3 19.3 - - - +
227M GLY* 3.7 20.0 - - - -
233M VAL* 4.2 5.8 - - - -
255M LEU* 3.9 36.8 - - + -
257M THR* 4.1 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 72 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M VAL* 4.7 6.3 - - - -
65M CYS* 5.5 3.1 - - - -
68M GLN 3.8 1.8 + - - -
69M GLU* 3.7 17.9 - - - -
71M CYS* 1.3 77.1 - - - +
73M VAL* 1.3 70.2 + - - +
75M LEU* 3.9 0.3 - - - +
76M GLU* 2.9 30.8 + - - +
93M GLY* 4.1 16.8 - - - -
94M PHE* 3.3 45.1 - - + +
97M THR* 3.8 23.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M TYR* 4.0 23.5 - - + +
38M MET* 4.1 25.7 - - + +
39M MET* 3.7 27.6 - - + +
42M VAL* 5.1 1.8 - - + -
69M GLU* 3.1 19.7 + - + +
72M CYS* 1.3 83.6 - - - +
74M GLY* 1.3 63.2 + - - +
76M GLU* 3.6 3.7 + - - +
77M ALA* 3.1 21.0 + - - +
97M THR* 4.2 14.1 - - + -
230M ILE* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M ALA 3.0 23.4 + - - -
73M VAL* 1.3 79.1 - - - +
75M LEU* 1.3 63.3 + - - +
77M ALA* 3.2 17.3 + - - +
78M GLY 3.3 4.9 + - - -
230M ILE* 3.8 21.5 - - - +
233M VAL* 4.0 9.9 - - - -
234M ARG* 3.5 11.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M CYS* 2.7 14.5 + - + +
72M CYS 3.9 2.7 - - - +
74M GLY* 1.3 75.1 - - - +
76M GLU* 1.3 58.5 + - - +
78M GLY* 2.8 23.9 + - - -
79M ILE* 3.4 11.7 + - - +
85M LEU* 4.6 2.0 - - + -
94M PHE* 3.7 30.7 - - + -
162M LEU* 3.9 24.9 - - + -
164M LEU* 4.3 9.0 - - + -
192M ILE* 4.2 10.8 - - + -
233M VAL* 3.3 27.6 - - + -
237M THR* 3.4 24.4 - - - +
253M MET* 3.9 5.2 - - + -
255M LEU* 3.5 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M MET* 5.6 7.6 - - + -
72M CYS 2.9 18.6 + - - +
73M VAL* 3.8 4.7 - - - +
75M LEU* 1.3 74.8 - - - +
77M ALA* 1.3 56.4 + - - +
78M GLY 3.3 0.2 + - - -
79M ILE* 3.1 37.1 + - - +
81M PRO* 4.7 6.4 - - - +
85M LEU* 5.4 4.4 - - - +
94M PHE* 5.9 0.3 - - - -
97M THR* 3.3 43.9 + - - +
98M ARG* 3.0 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M TYR* 3.5 38.3 + - + +
73M VAL 3.1 14.5 + - - +
74M GLY* 3.3 13.5 - - - +
75M LEU 3.0 0.8 + - - -
76M GLU* 1.3 78.6 - - - +
78M GLY* 1.3 56.3 + - - +
79M ILE 3.5 0.9 - - - -
234M ARG* 3.8 13.2 - - + +
238M ARG* 3.3 21.3 + - - -
----------------------------------------------------------
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