Contacts of the helix formed by residues 75 - 83 (chain X) in PDB entry 3GX4
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 GLU 75 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56X TRP* 6.2 0.7 - - - -
66X ILE* 3.7 15.3 - - + +
67X SER 3.7 10.1 - - - -
68X LYS* 3.1 52.5 + - - +
69X ARG* 3.6 43.5 - - - +
72X SER 3.9 6.8 + - - +
73X ALA* 3.0 14.9 + - - +
74X GLY* 1.4 61.4 - - - -
76X GLN* 1.4 65.5 + - - +
77X ARG* 2.8 3.8 - - - +
78X GLN* 3.3 16.9 + - - +
79X LYS 3.5 7.4 + - - -
97X TYR* 4.3 10.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73X ALA* 2.8 23.2 + - + +
74X GLY* 3.9 4.0 - - - +
75X GLU* 1.4 70.8 - - - +
77X ARG* 1.3 66.5 + - - +
79X LYS* 2.9 13.2 + - - +
80X ASP* 2.8 58.3 + - - +
97X TYR* 2.7 39.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56X TRP* 4.2 23.3 - - + -
74X GLY* 2.6 31.7 + - - +
75X GLU* 2.8 1.5 - - - -
76X GLN* 1.3 82.2 - - - +
78X GLN* 1.4 61.3 - - - +
80X ASP* 3.3 13.1 + - + +
81X ARG* 3.1 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25X TYR* 5.2 0.7 + - - -
56X TRP* 3.7 14.4 + - + -
57X HIS* 2.9 38.5 + - - +
59X VAL 2.7 30.2 + - - +
60X ILE* 3.7 7.3 - - - +
66X ILE* 3.4 23.2 - - + +
67X SER 4.6 1.9 + - - -
69X ARG* 2.5 35.2 + - - +
75X GLU* 3.3 13.2 + - - +
76X GLN 3.2 0.4 - - - -
77X ARG* 1.4 74.8 - - - +
79X LYS* 1.3 66.6 + - - +
81X ARG* 3.1 6.4 + - - +
82X LEU* 2.9 26.9 + - + +
207Y 6OG 3.8 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66X ILE* 3.7 12.3 - - + +
75X GLU 3.5 1.8 + - - -
76X GLN* 2.9 10.7 + - - +
78X GLN* 1.3 73.7 - - - +
80X ASP* 1.4 71.6 + - - +
81X ARG 2.6 15.6 + - - -
82X LEU* 3.2 0.8 + - - -
83X GLU* 2.9 60.1 + - - +
89X ILE* 3.8 21.3 - - + +
91X GLN* 5.1 8.1 - - - -
97X TYR* 3.3 57.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76X GLN* 2.8 53.6 + - - +
77X ARG* 3.8 9.3 + - + +
78X GLN 3.3 0.4 - - - -
79X LYS* 1.4 88.2 + - - +
81X ARG* 1.3 58.7 + - + +
83X GLU* 4.0 8.1 - - - +
84X GLU* 3.4 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X THR 5.2 5.5 + - - -
54X VAL 5.0 1.6 + - - -
56X TRP* 3.4 41.1 - - + +
57X HIS* 3.4 42.7 + - + -
77X ARG* 3.1 25.0 - - + +
78X GLN* 3.1 11.2 - - - +
79X LYS 2.6 2.4 - - - -
80X ASP* 1.3 82.8 - - + +
82X LEU* 1.3 60.1 + - - +
83X GLU 3.1 1.3 - - - -
84X GLU* 2.8 43.4 + - - +
85X GLU* 3.5 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20X GLY* 6.4 0.2 - - - -
21X LYS 5.1 0.7 - - - +
22X VAL* 3.4 29.8 - - + -
57X HIS* 3.4 35.2 - - + +
58X ARG* 4.4 3.6 - - + -
60X ILE* 4.9 5.4 - - + -
66X ILE* 4.4 11.9 - - + -
78X GLN* 2.9 30.0 + - + +
79X LYS* 3.9 6.7 - - - +
81X ARG* 1.3 76.2 - - - +
83X GLU* 1.3 58.8 - - - +
85X GLU* 3.0 20.6 + - - +
87X VAL* 3.0 41.4 + - + +
89X ILE* 3.9 14.1 - - + -
99X LEU* 5.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79X LYS* 2.9 54.4 + - - +
80X ASP* 4.0 7.1 - - - +
82X LEU* 1.3 71.1 - - - +
84X GLU* 1.3 58.3 + - - +
85X GLU 2.8 4.5 - - - -
86X GLY* 2.8 20.1 + - - -
87X VAL 3.7 14.4 - - - +
89X ILE* 3.6 28.4 + - + +
91X GLN* 5.7 0.2 - - - +
----------------------------------------------------------
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