Contacts of the helix formed by residues 76 - 85 (chain A) in PDB entry 1T6S
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 PHE 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.6 40.8 - - + -
72A THR* 5.4 4.0 - - + -
73A GLU* 2.9 27.4 + - + +
75A GLU* 1.3 112.7 - - + +
77A ALA* 1.3 64.5 + - - +
78A ASP 3.2 2.7 - - - -
79A LEU* 3.1 31.5 + - + +
80A VAL* 3.0 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU 3.9 1.7 + - - -
74A PRO* 3.1 25.3 + - + +
75A GLU 3.5 0.6 - - - -
76A PHE* 1.3 76.9 - - - +
78A ASP* 1.3 58.0 + - - +
80A VAL* 3.4 6.5 + - - +
81A ARG* 3.0 23.8 + - - +
422B NO3 3.4 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU 5.2 0.6 + - - +
76A PHE* 3.2 0.8 - - - +
77A ALA* 1.3 78.6 - - - +
79A LEU* 1.3 68.1 + - + +
81A ARG* 3.3 14.3 + - - +
82A GLN* 2.7 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 3.1 35.7 + - + +
78A ASP* 1.3 78.9 - - + +
80A VAL* 1.3 66.3 + - + +
82A GLN* 3.2 29.9 + - - +
83A LEU* 3.2 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.6 29.6 - - + +
76A PHE* 3.0 22.7 + - + +
77A ALA* 3.8 7.6 - - - +
79A LEU* 1.3 76.3 - - + +
81A ARG* 1.3 58.0 + - - +
83A LEU* 3.1 5.1 + - + -
84A LEU* 2.8 68.1 + - + +
138B ARG* 5.0 1.8 - - - -
422B NO3 3.8 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 3.0 13.5 + - - +
78A ASP* 3.5 15.2 + - - +
79A LEU 3.2 0.2 - - - -
80A VAL* 1.3 77.6 - - - +
82A GLN* 1.3 57.4 + - + +
84A LEU* 5.3 0.2 - - - -
85A ALA* 2.9 44.9 + - + +
87A VAL* 5.4 1.2 - - - +
90A ARG* 3.2 41.9 - - - +
405A NO3 5.5 0.6 + - - -
105B TRP 4.7 2.2 + - - -
106B HIS* 4.7 4.6 + - - +
107B GLN 3.4 22.4 + - - +
108B PRO* 4.2 4.7 - - - +
422B NO3 3.2 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 2.7 39.4 + - - +
79A LEU* 3.2 20.0 + - - +
81A ARG* 1.3 76.3 - - + +
83A LEU* 1.3 59.5 + - - +
86A PRO* 3.5 20.6 - - - +
405A NO3 3.7 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 3.2 9.6 + - - +
80A VAL* 3.1 10.0 + - + +
81A ARG 3.1 0.2 - - - -
82A GLN* 1.3 77.9 - - - +
84A LEU* 1.3 79.3 + - + +
85A ALA 3.4 0.2 - - - -
86A PRO* 3.8 8.5 - - - +
89A GLN* 4.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 2.8 46.1 + - + +
81A ARG* 5.3 1.1 - - - -
83A LEU* 1.3 95.9 - - + +
85A ALA* 1.3 60.4 + - + +
86A PRO* 3.7 1.8 - - - -
89A GLN* 2.9 19.2 + - - +
408A NO3 4.0 1.7 + - - -
136B GLU* 5.1 2.5 - - - +
138B ARG* 3.6 44.0 + - - +
152B THR* 5.1 0.5 + - - -
154B GLU* 6.2 0.2 - - - -
157B LEU* 4.3 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 2.9 21.0 + - + +
84A LEU* 1.3 82.4 - - - +
86A PRO* 1.3 63.0 - - - +
87A VAL 3.7 0.5 + - - -
89A GLN* 3.8 4.9 - - - +
90A ARG* 2.9 26.8 + - - +
405A NO3 4.3 0.5 + - - -
408A NO3 3.8 2.5 - - - +
107B GLN* 3.5 39.7 - - + +
138B ARG* 4.7 0.4 - - - +
422B NO3 4.7 7.0 - - - +
----------------------------------------------------------
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