Contacts of the helix formed by residues 67 - 79 (chain c) in PDB entry 3J7Y
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 ASP 67 (chain c).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64b TYR* 3.1 11.1 + - + +
66c TRP* 1.3 74.2 - - - +
68c TYR* 1.3 67.4 + - - +
69c HIS* 3.5 7.5 + - - +
70c ALA* 3.8 17.6 - - + +
71c GLU* 3.0 33.5 + - - +
153h LYS* 3.0 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61c SER* 5.2 2.2 - - - -
66c TRP* 3.9 36.5 + + + +
67c ASP* 1.3 75.5 + - - +
69c HIS* 1.3 64.5 + - - +
71c GLU* 3.2 3.4 + - - +
72c ILE* 2.9 53.7 + - + +
89c LYS* 4.2 20.3 + - + -
92c PHE* 3.6 12.3 - - - +
93c VAL* 5.4 0.9 - - - +
178c LEU* 3.1 30.9 + - + +
180c LEU* 3.3 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67c ASP* 4.2 7.6 + - - +
68c TYR* 1.3 83.7 - - - +
70c ALA* 1.3 60.7 + - + +
72c ILE* 3.2 5.7 + - - +
73c GLN* 2.9 58.5 + - + +
85c LEU* 3.7 22.5 - - + +
89c LYS* 3.9 29.3 + - - +
153h LYS* 6.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62b VAL* 4.4 14.5 - - + +
67c ASP* 3.6 23.6 + - + +
68c TYR 3.3 0.4 - - - -
69c HIS* 1.3 84.2 - - + +
71c GLU* 1.3 56.9 + - - +
73c GLN* 3.2 9.8 + - - +
74c ALA* 2.9 27.4 + - - +
150h PRO* 3.7 24.9 - - - +
151h ASN* 5.9 0.3 + - - -
153h LYS* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28b ARG* 2.7 36.1 + - - +
62b VAL* 3.8 18.6 - - + -
64b TYR* 2.7 27.6 + - - +
66c TRP* 2.9 36.2 - - + -
67c ASP 3.0 19.9 + - - +
68c TYR 3.8 3.4 - - - +
70c ALA* 1.3 76.6 - - - +
72c ILE* 1.3 55.9 - - - +
74c ALA* 3.2 6.9 + - - +
75c PHE* 2.9 28.9 + - - +
78c ARG* 5.1 3.1 + - - +
178c LEU* 4.0 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68c TYR* 2.9 38.3 + - + +
69c HIS* 3.5 11.2 - - - +
71c GLU* 1.3 75.5 - - - +
73c GLN* 1.3 56.8 + - - +
75c PHE* 3.2 4.5 + - - +
76c GLY* 2.9 26.3 + - - -
85c LEU* 4.0 23.2 - - + +
88c LEU* 3.8 19.0 - - + +
89c LYS* 3.5 23.8 - - + +
92c PHE* 3.8 24.7 - - + -
178c LEU* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69c HIS* 2.9 46.6 + - + +
70c ALA* 3.4 11.0 - - - +
72c ILE* 1.3 76.2 - - - +
74c ALA* 1.3 57.5 + - - +
76c GLY* 3.2 2.3 + - - -
77c HIS* 2.9 48.6 + - + +
85c LEU* 3.5 32.4 - - + +
150h PRO* 3.1 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59b PRO 3.6 15.5 - - - +
60b GLY* 3.6 24.2 - - - +
62b VAL* 4.0 23.1 - - + -
70c ALA 2.9 13.4 + - - +
71c GLU 3.3 9.0 - - - +
73c GLN* 1.3 75.1 - - - +
75c PHE* 1.3 58.1 + - - +
77c HIS* 3.2 4.5 + - - +
78c ARG* 2.9 33.8 + - - +
151h ASN* 4.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71c GLU 2.9 13.3 + - - +
72c ILE 3.2 8.5 - - - +
74c ALA* 1.3 76.9 - - - +
76c GLY* 1.3 67.3 + - - +
78c ARG* 3.2 34.4 + - - +
79c LEU* 3.5 36.3 + - + +
83c PHE* 4.3 10.3 - + - -
88c LEU* 4.4 14.4 - - + -
92c PHE* 4.4 9.2 - + - -
173c LEU* 4.3 16.4 - - + -
174c ALA 3.8 17.9 - - - -
175c VAL* 4.1 22.4 - - + -
178c LEU* 3.4 26.2 - - + -
198c VAL* 4.5 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72c ILE 2.9 13.2 + - - -
73c GLN* 3.2 4.5 + - - -
75c PHE* 1.3 78.0 - - - +
77c HIS* 1.3 65.7 + - - +
79c LEU* 3.8 6.4 + - - +
81c GLU 3.2 24.5 + - - +
82c ASN* 5.5 3.6 - - - -
83c PHE* 4.0 28.2 - - - -
85c LEU* 5.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 77 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59b PRO* 3.8 44.3 - - + +
60b GLY* 5.0 0.9 - - - -
73c GLN* 2.9 46.9 + - + +
74c ALA 3.2 6.5 + - - +
76c GLY* 1.3 76.2 - - - +
78c ARG* 1.3 64.1 + - - +
80c GLN* 3.1 17.5 + - - +
82c ASN* 5.9 9.0 - - + +
150h PRO* 5.1 7.5 - - + +
151h ASN* 5.2 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23b VAL* 3.8 26.0 - - + +
24b GLN* 4.0 22.5 + - + +
26b LEU 4.8 0.8 + - - -
27b GLN* 3.7 31.3 + - - +
60b GLY* 3.3 36.7 + - - +
62b VAL* 5.0 2.2 - - - +
80b LEU* 3.3 35.4 - - - +
71c GLU* 5.1 3.4 + - - +
74c ALA* 2.9 19.0 + - - +
75c PHE* 3.2 27.6 + - - +
77c HIS* 1.3 77.0 - - - +
79c LEU* 1.3 71.7 + - + +
80c GLN* 3.1 12.7 + - - +
173c LEU* 3.4 12.3 + - - -
174c ALA* 3.8 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21b ARG* 2.4 36.5 + - - +
23b VAL* 5.0 7.4 - - + -
75c PHE* 3.5 43.9 + - + +
76c GLY 3.8 2.7 + - - +
77c HIS 3.3 1.0 + - - -
78c ARG* 1.3 85.8 - - + +
80c GLN* 1.3 63.2 + - - +
81c GLU* 3.2 21.1 - - - +
83c PHE* 4.8 4.9 - - + -
173c LEU* 3.4 31.9 - - + +
198c VAL* 5.8 2.0 - - + -
214c PHE* 3.5 26.7 - - + -
218c PHE* 4.3 8.3 - - + -
----------------------------------------------------------
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