Contacts of the helix formed by residues 76 - 87 (chain D) in PDB entry 3GTU
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 SER 76 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 3.6 36.7 - - - +
20D ILE* 4.5 6.5 - - - +
64D PRO* 3.6 31.4 - - - +
75D GLN* 1.3 70.6 + - - +
77D ASN* 1.3 65.6 + - - +
79D ILE* 3.0 6.4 + - - +
80D LEU* 3.0 36.1 + - - +
108D MET* 5.7 3.6 - - - -
111D ARG* 5.6 3.1 - - - -
162D LEU* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ASN* 3.5 25.4 + - - +
75D GLN 3.4 0.8 - - - -
76D SER* 1.3 77.3 - - - +
78D ALA* 1.3 57.3 + - - +
80D LEU* 4.0 9.9 - - - +
81D ARG* 3.0 37.2 + - - +
104D GLU* 3.4 42.0 + - - +
105D ASN* 5.5 2.6 + - - -
108D MET* 3.3 34.1 - - - +
111D ARG* 4.8 1.7 + - - -
158D PHE* 5.9 0.4 - - - -
162D LEU* 4.3 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE* 5.9 0.7 - - + +
97C ASP* 3.7 33.0 - - + +
98C ILE 3.8 11.2 - - - +
101C ASN* 4.0 2.0 - - - +
73D ILE* 3.7 12.4 - - + +
74D THR 3.2 14.8 - - - +
75D GLN* 3.0 14.4 + - + +
77D ASN* 1.3 76.5 - - - +
79D ILE* 1.3 59.9 + - - +
81D ARG* 3.6 1.6 + - - +
82D TYR* 3.0 29.5 + - - +
85D ARG* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 4.7 1.1 - - + -
20D ILE* 3.7 32.1 - - + -
64D PRO* 3.5 45.3 - - + +
65D TYR* 4.0 14.6 - - - -
66D LEU* 3.8 26.2 - - + +
73D ILE* 4.2 19.7 - - + +
75D GLN 3.0 12.9 + - - +
76D SER 3.0 6.4 + - - +
78D ALA* 1.3 75.9 - - - +
80D LEU* 1.3 57.0 + - - +
82D TYR* 3.1 9.2 + - - +
83D ILE* 3.0 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU 5.8 0.7 - - - +
19D ALA* 3.9 28.0 - - + +
20D ILE* 4.0 20.4 - - + -
23D LEU* 3.7 26.8 - - + +
76D SER* 3.0 27.2 + - - +
77D ASN* 4.0 6.7 - - - +
79D ILE* 1.3 73.3 - - - +
81D ARG* 1.3 60.5 + - - +
83D ILE* 3.5 0.8 + - - -
84D ALA* 2.9 34.2 + - - +
158D PHE* 4.2 20.0 - - + +
161D PHE* 5.3 1.3 - - + -
162D LEU* 3.5 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 3.7 27.8 - - - +
97C ASP* 3.3 36.6 - - - +
100C GLU* 4.7 0.8 + - - -
101C ASN* 6.0 1.3 - - - +
77D ASN* 3.0 25.5 + - - +
78D ALA 3.9 0.4 - - - +
80D LEU* 1.3 74.6 - - - +
82D TYR* 1.3 56.7 - - - +
84D ALA* 3.9 4.2 - - - +
85D ARG* 2.9 37.8 + - - +
90D CYS* 4.6 8.2 - - - +
100D VAL* 4.6 2.6 - - - +
101D ASP* 3.0 29.9 + - - +
104D GLU* 2.8 39.7 + - - +
158D PHE* 3.5 32.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 3.5 21.5 - - - -
94C ILE* 3.8 29.6 - - + -
6D MET* 5.1 1.6 - - + -
66D LEU* 4.0 17.5 - - + -
68D ASP* 2.6 39.2 + - + +
71D ASN* 3.2 19.9 + - + -
73D ILE* 3.8 24.2 - - + -
78D ALA 3.0 19.6 + - - +
79D ILE* 3.2 5.8 - - - +
81D ARG* 1.3 80.4 - - - +
83D ILE* 1.3 66.1 + - + +
85D ARG* 3.5 21.8 - - - +
86D LYS* 3.1 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D MET* 5.1 2.9 - - + -
20D ILE* 3.9 9.4 - - + +
23D LEU* 4.1 20.6 - - + -
24D LEU* 3.7 38.4 - - + -
27D THR* 4.3 3.6 - - - +
29D THR* 4.3 5.8 - - + +
66D LEU* 3.9 17.7 - - + -
79D ILE* 3.0 33.2 + - + +
80D LEU* 5.0 0.2 - - - -
82D TYR* 1.3 73.3 - - + +
84D ALA* 1.3 66.2 - - - +
86D LYS* 3.2 20.5 + - + +
87D HIS* 3.1 40.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 4.0 8.2 - - + +
80D LEU 2.9 19.9 + - - +
81D ARG 3.9 2.0 - - - +
83D ILE* 1.3 76.6 - - - +
85D ARG* 1.3 57.9 + - - +
87D HIS* 2.8 21.5 + - - -
89D MET* 3.0 46.4 + - + +
90D CYS* 4.2 1.1 - - - -
158D PHE* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 4.0 23.6 + - - +
93C GLN* 3.1 52.1 + - - +
94C ILE* 4.2 3.6 - - - +
97C ASP* 2.7 31.5 + - - -
78D ALA 4.9 0.2 + - - -
81D ARG* 2.9 31.1 + - - +
82D TYR* 3.5 24.1 + - - +
83D ILE 3.3 0.2 - - - -
84D ALA* 1.3 74.6 - - - +
86D LYS* 1.3 63.8 + - + +
88D ASN* 3.1 14.3 + - - +
89D MET 4.9 0.4 - - - +
90D CYS* 4.3 15.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 3.2 27.2 + - - +
6D MET* 5.2 10.1 - - + -
68D ASP* 4.1 9.4 + - - -
71D ASN* 5.4 0.2 + - - -
82D TYR* 3.1 47.0 + - + +
83D ILE* 3.4 13.9 - - + +
84D ALA 3.1 0.6 - - - -
85D ARG* 1.3 76.9 - - + +
87D HIS* 1.3 69.7 + - + +
88D ASN 3.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D THR* 3.4 44.9 + - + -
29D THR* 2.9 28.2 + - - +
83D ILE* 3.1 30.8 + - + +
84D ALA* 2.8 7.1 + - - +
86D LYS* 1.3 87.6 + - + +
88D ASN* 1.3 70.5 + - - +
89D MET* 3.1 14.6 + - + +
----------------------------------------------------------
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