Contacts of the helix formed by residues 68 - 78 (chain W) 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 W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65W CYS* 2.8 21.7 + - + +
67W GLY* 1.3 81.0 - - - +
69W GLU* 1.3 55.2 + - - +
70W ALA* 2.9 6.5 - - - -
71W CYS* 2.8 29.5 + - + +
72W CYS* 3.8 4.3 + - - -
90W ARG* 3.7 18.5 - - - +
194W GLU* 3.0 33.6 - - - +
196W ASN* 3.0 29.9 - - - +
227W GLY 5.2 0.4 - - - -
257W THR* 3.6 28.2 - - + +
258W TYR 4.3 5.6 - - - +
259W ARG* 3.1 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39W MET* 3.6 34.6 - - + +
42W VAL* 3.5 28.3 - - + +
43W ARG* 2.5 57.9 + - - -
65W CYS 4.0 1.8 - - - +
66W ASP* 3.2 13.7 - - - -
67W GLY 2.8 14.7 + - - -
68W GLN* 1.3 76.6 + - - +
70W ALA* 1.3 59.9 + - - +
71W CYS 3.0 2.1 + - - -
72W CYS* 4.2 9.2 - - - -
73W VAL* 3.2 28.4 + - + +
287W PRO* 3.6 4.6 - - + +
288W ILE* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39W MET* 4.2 9.0 - - - -
68W GLN 2.8 0.6 + - - -
69W GLU* 1.3 78.9 - - - +
71W CYS* 1.3 58.7 + - - +
74W GLY* 3.1 19.8 + - - +
227W GLY 3.0 24.9 - - - +
228W MET 3.7 10.8 - - - +
229W ASP 4.1 0.4 - - - -
230W ILE* 3.7 27.8 - - + +
233W VAL* 3.3 15.6 - - - +
287W PRO* 3.8 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68W GLN* 2.8 14.6 + - - +
70W ALA* 1.3 79.6 - - - +
72W CYS* 1.3 61.1 + - - +
75W LEU* 2.7 39.6 + - + +
94W PHE* 4.9 0.4 - - + -
194W GLU* 4.1 21.1 - - - +
227W GLY* 3.8 19.7 - - - -
233W VAL* 3.8 5.3 - - - +
255W LEU* 3.7 38.1 - - + -
257W THR* 4.3 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 72 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42W VAL* 4.5 7.4 - - - -
65W CYS* 5.1 4.7 - - - -
68W GLN 3.8 2.0 + - - -
69W GLU* 4.1 19.3 - - - -
71W CYS* 1.3 79.6 - - - +
73W VAL* 1.3 63.5 + - - +
75W LEU* 4.2 0.9 - - - +
76W GLU* 3.2 18.4 + - - +
93W GLY* 3.9 27.1 - - - -
94W PHE* 3.5 41.3 - - + -
97W THR* 3.2 26.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W TYR* 4.0 20.2 - - + +
38W MET* 4.0 33.9 - - + +
39W MET* 3.5 26.9 - - + +
42W VAL* 5.2 1.1 - - + -
69W GLU* 3.2 19.2 + - + +
71W CYS 3.2 0.4 - - - -
72W CYS* 1.3 81.1 - - - +
74W GLY* 1.3 60.6 + - - +
75W LEU 3.2 0.2 - - - -
76W GLU* 3.3 6.0 + - - +
77W ALA* 2.9 27.2 + - - +
97W THR* 4.3 12.8 - - + -
230W ILE* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70W ALA 3.1 16.5 + - - -
73W VAL* 1.3 76.2 - - - +
75W LEU* 1.3 64.5 + - - +
77W ALA* 3.1 14.1 + - - +
78W GLY* 3.3 9.2 + - - -
230W ILE* 3.2 23.1 - - - +
233W VAL* 3.4 14.8 - - - +
234W ARG* 3.6 11.5 - - - -
237W THR* 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71W CYS* 2.7 21.7 + - + +
72W CYS* 4.2 3.6 - - - +
74W GLY* 1.3 72.7 - - - +
76W GLU* 1.3 63.7 + - - +
78W GLY 3.1 10.4 + - - -
79W ILE* 3.6 20.5 + - - +
85W LEU* 4.9 3.4 - - + -
94W PHE* 3.8 28.0 - - + -
162W LEU* 3.8 19.3 - - + -
164W LEU* 4.3 7.2 - - + -
192W ILE* 4.0 17.0 - - + -
233W VAL* 3.4 25.6 - - + +
237W THR* 3.4 18.4 - - - +
253W MET* 3.8 9.9 - - + -
255W LEU* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38W MET* 5.6 7.2 - - + -
72W CYS 3.2 18.1 + - - +
73W VAL* 3.3 5.4 + - - +
75W LEU* 1.3 80.9 - - - +
77W ALA* 1.3 58.8 + - - +
79W ILE* 3.2 29.6 - - - +
81W PRO* 4.2 9.0 - - - +
85W LEU* 4.8 4.9 - - - +
97W THR* 3.2 37.4 + - - +
98W ARG* 2.7 48.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W LYS* 6.1 1.3 - - - +
35W TYR* 3.5 38.0 + - + +
73W VAL 2.9 17.0 + - - +
74W GLY* 3.4 9.6 - - - +
75W LEU 3.1 0.8 - - - -
76W GLU* 1.3 75.8 - - - +
78W GLY* 1.3 59.4 + - - +
79W ILE 3.5 1.1 + - - -
230W ILE* 5.2 0.2 - - + -
234W ARG* 3.7 13.2 - - + +
238W ARG* 3.3 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74W GLY 3.3 4.2 + - - -
75W LEU 3.1 5.5 + - - -
77W ALA* 1.3 79.1 - - - +
79W ILE* 1.3 67.2 + - - +
234W ARG 4.3 1.3 - - - -
237W THR* 3.5 27.7 - - - +
238W ARG* 3.8 25.8 - - - +
241W ALA* 4.2 6.6 - - - +
245W ARG* 4.9 1.2 + - - -
----------------------------------------------------------
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