Contacts of the helix formed by residues 76 - 83 (chain A) in PDB entry 1TTV
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 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 3.3 6.1 + - - -
60A LYS* 4.1 8.5 - - - +
62A LEU* 2.7 46.5 - - + +
73A CYS* 3.7 20.4 - - + +
74A SER 3.3 4.9 + - - +
75A ASN* 1.3 76.6 - - - +
77A PRO* 1.3 77.9 - - - +
78A LEU* 3.0 25.0 + - - +
79A GLY* 3.0 14.6 + - - +
80A GLU* 3.1 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.5 14.8 - - + +
33A LEU* 3.4 18.2 - - + -
56A TYR* 2.9 26.2 - - + +
60A LYS* 5.8 0.9 - - + -
75A ASN 4.9 0.2 - - - +
76A ASP* 1.3 88.0 - - - +
78A LEU* 1.3 56.8 + - - -
80A GLU* 3.1 26.8 - - + +
81A LEU* 3.2 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.8 14.8 - - + +
53A LEU* 3.2 26.5 - - + -
56A TYR* 3.6 11.1 + - + -
57A ILE* 4.2 12.1 - - + -
62A LEU* 3.9 18.2 - - + -
76A ASP* 3.0 15.7 + - - +
77A PRO* 1.3 77.6 - - - +
79A GLY* 1.3 64.6 + - - +
81A LEU* 2.9 12.8 + - + +
82A PHE* 3.0 57.1 + - + -
87A PHE* 3.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A CYS 4.5 7.2 - - - -
76A ASP* 3.0 10.6 + - - +
78A LEU* 1.3 80.9 - - - +
80A GLU* 1.3 56.7 + - - +
82A PHE* 5.1 3.4 - - - -
83A GLY* 2.8 26.3 + - - -
84A VAL* 3.1 29.2 + - - -
85A GLN* 4.1 10.6 + - - -
87A PHE* 5.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 2.8 31.3 - - + +
74A SER 5.5 0.6 + - - +
76A ASP 3.1 9.2 + - - +
77A PRO* 3.1 27.4 - - + +
79A GLY* 1.3 75.9 - - - +
81A LEU* 1.3 61.4 + - - +
83A GLY* 3.8 7.6 + - - -
85A GLN* 4.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.4 24.2 - - + +
29A LEU* 3.3 31.0 - - + -
30A LEU* 3.5 35.2 - - + -
33A LEU* 4.2 4.9 - - + -
77A PRO 3.2 5.4 + - - +
78A LEU 2.9 9.1 + - - +
80A GLU* 1.3 79.7 - - - +
82A PHE* 1.3 74.8 + - + +
83A GLY* 3.1 2.7 + - - -
102A ASN* 2.9 37.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 5.1 0.4 - - + -
53A LEU* 4.0 9.6 - - + -
78A LEU* 3.0 54.7 + - + +
79A GLY* 4.3 1.1 - - - +
81A LEU* 1.3 85.3 - - + +
83A GLY* 1.3 59.6 + - - +
84A VAL* 3.9 17.7 - - + +
87A PHE* 4.0 17.5 - + - -
98A MET* 3.2 55.1 - - + +
99A ILE* 3.8 19.3 - - + -
102A ASN* 3.4 26.9 - - - +
120A IMY 4.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY 2.8 8.7 + - - -
80A GLU* 4.2 7.6 - - - -
81A LEU 3.1 4.1 - - - -
82A PHE* 1.3 76.8 - - - +
84A VAL* 1.3 71.8 + - - +
----------------------------------------------------------
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