Contacts of the helix formed by residues 64 - 77 (chain D) in PDB entry 3T79
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 PRO 64 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ILE* 4.0 19.1 - - + -
60D ILE* 2.9 13.4 - - + +
61D ALA 3.2 20.4 - - - +
62D LYS 3.5 4.0 - - - +
63D ASP* 1.3 90.2 - - - +
65D LEU* 1.3 67.3 + - + +
66D PRO* 3.5 0.7 - - - -
67D THR* 3.1 9.2 - - - -
68D CYS* 3.0 24.6 + - - -
95D LEU* 5.7 0.2 - - + -
96D VAL* 4.0 32.1 - - + -
99D LEU* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ASP* 3.3 6.8 - - - +
64D PRO* 1.3 77.9 - - + +
66D PRO* 1.3 74.5 - - + +
68D CYS* 3.1 8.3 + - + +
69D ASP* 3.0 44.5 + - - +
93D TYR* 4.4 18.6 - - + -
96D VAL* 4.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LEU* 4.6 26.4 - - + +
19D TYR* 4.5 4.0 - - - -
22D ILE* 5.0 5.4 - - + -
63D ASP* 3.3 36.6 - - - +
64D PRO 3.5 0.7 - - - -
65D LEU* 1.3 94.8 - - + +
67D THR* 1.3 58.2 - - - +
69D ASP* 3.6 7.4 + - + +
70D ALA* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE* 4.1 30.5 - - + +
50D ILE* 5.4 0.4 - - + -
53D TYR* 4.4 12.6 - - + -
54D ILE* 4.0 24.2 - - + -
60D ILE* 3.4 24.0 - - + +
63D ASP 4.4 2.9 + - - -
64D PRO 3.1 10.5 + - - -
66D PRO* 1.3 77.3 - - - +
68D CYS* 1.3 58.9 + - - +
70D ALA* 3.3 7.1 + - - +
71D MET* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ILE* 3.8 22.0 - - - -
64D PRO* 3.0 16.3 + - - -
65D LEU* 3.1 13.2 + - + +
67D THR* 1.3 78.9 - - - +
69D ASP* 1.3 62.7 + - - +
71D MET* 3.3 5.5 + - - +
72D ILE* 2.9 33.7 + - + +
92D LEU* 3.7 34.4 - - + +
93D TYR* 5.0 5.6 - - + -
95D LEU* 5.8 0.9 - - - -
96D VAL* 4.0 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D TYR* 4.1 12.7 + - + +
65D LEU* 3.0 30.4 + - - +
66D PRO* 3.8 5.5 - - + +
68D CYS* 1.3 74.1 - - - +
70D ALA* 1.3 68.0 + - - +
72D ILE* 2.9 10.9 + - - +
73D TRP* 2.9 23.6 + - - +
93D TYR* 3.8 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D TYR* 3.5 35.6 + - + -
22D ILE* 4.2 16.4 - - + -
66D PRO 2.9 19.0 + - - +
67D THR 3.5 5.6 - - - +
69D ASP* 1.3 75.7 - - - +
71D MET* 1.3 55.1 + - - +
73D TRP* 3.3 2.1 + - - +
74D PHE* 2.5 51.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE* 3.8 27.4 - - + +
23D TRP* 5.1 4.5 - - + -
26D TYR* 3.5 39.5 - - + -
45D LEU* 4.1 28.6 - - + +
50D ILE* 3.9 35.7 - - + -
67D THR* 2.9 25.5 + - + +
68D CYS* 3.4 6.5 - - - +
70D ALA* 1.3 74.6 - - - +
72D ILE* 1.3 66.2 + - - +
73D TRP 3.2 0.2 + - - -
74D PHE* 3.2 13.3 + - + +
75D SER* 2.9 25.9 + - - -
88D LEU* 5.2 1.8 - - + -
92D LEU* 4.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D CYS 2.9 21.2 + - - +
69D ASP* 2.9 13.6 + - - +
71D MET* 1.3 71.6 - - - +
73D TRP* 1.3 57.3 + - - +
75D SER* 3.3 5.9 - - - -
76D ARG* 2.9 55.3 + - - +
85D VAL* 3.6 18.2 - - + +
88D LEU* 4.4 7.9 - - + -
89D GLN* 3.7 47.6 - - + +
92D LEU* 4.3 12.1 - - + -
93D TYR* 4.3 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 4.5 6.3 - - + -
7D LEU* 3.3 38.6 - - + -
8D LEU* 3.7 28.3 - - + -
10D GLU* 6.3 0.7 - - + -
11D LEU* 4.0 15.0 - - + +
19D TYR* 3.7 30.7 - + + +
69D ASP 2.9 11.0 + - - +
70D ALA 3.3 8.3 - - - +
72D ILE* 1.3 72.8 - - - +
74D PHE* 1.3 93.4 + + - +
75D SER 2.9 0.7 + - - -
76D ARG* 3.0 14.4 + - + +
77D ALA* 2.4 56.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 4.5 16.4 - - + -
8D LEU* 4.8 7.6 - - + -
19D TYR* 3.5 39.5 - + + -
20D ARG* 5.8 0.2 - - - -
22D ILE* 4.9 5.4 - - + -
23D TRP* 4.0 37.5 - + + -
45D LEU* 4.0 15.0 - - + -
70D ALA* 2.5 60.4 + - + +
71D MET* 3.8 13.2 - - + +
73D TRP* 1.3 94.2 - + - +
75D SER* 1.3 63.5 + - - +
77D ALA* 2.9 6.4 + - - -
78D LEU* 2.7 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LEU* 4.1 15.5 - - - +
71D MET 2.9 18.2 + - - -
72D ILE* 3.3 8.3 - - - -
73D TRP 2.9 0.4 + - - -
74D PHE* 1.3 81.7 - - - +
76D ARG* 1.3 60.3 + - - -
78D LEU* 2.8 21.2 + - - +
80D ILE* 3.4 28.8 - - - +
85D VAL* 3.5 21.5 - - - +
88D LEU* 5.1 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ILE* 2.9 46.8 + - - +
73D TRP* 3.5 14.7 - - + +
75D SER* 1.3 79.1 + - - +
77D ALA* 1.3 60.1 + - + +
78D LEU 2.9 13.6 - - - +
80D ILE* 4.9 6.7 - - - +
82D ASN* 4.3 10.0 + - - +
85D VAL* 4.0 32.2 - - + +
86D LEU* 5.6 3.6 - - - +
89D GLN* 4.8 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 5.6 4.0 - - + +
7D LEU* 4.1 21.3 - - + +
73D TRP* 2.4 71.4 + - + +
74D PHE* 3.2 7.0 - - - +
76D ARG* 1.3 73.6 - - + +
78D LEU* 1.3 61.2 + - + +
----------------------------------------------------------
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