Contacts of the helix formed by residues 93 - 100 (chain A) in PDB entry 7V3X
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 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 4.8 5.7 + - - -
84A ILE* 5.6 1.7 - - - +
88A ARG* 6.2 0.2 - - - -
91A GLY 3.9 2.8 + - - +
92A TRP* 1.3 70.9 - - - +
94A LEU* 1.3 62.5 + - - +
95A ALA* 3.6 15.5 + - - +
96A LYS* 3.2 34.8 + - + +
97A LEU* 3.7 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 4.3 20.6 - - + -
61A TYR* 4.1 33.0 - - + -
64A ILE* 6.5 0.4 - - + -
83A ILE* 4.2 15.7 - - + +
84A ILE* 4.2 21.5 + - + +
87A ALA* 3.6 30.9 - - + +
92A TRP* 3.9 6.1 + - + +
93A ASP* 1.3 69.9 + - - +
95A ALA* 1.3 60.1 + - - +
96A LYS 3.3 0.2 - - - -
97A LEU* 3.2 7.0 + - + +
98A VAL* 2.9 34.8 + - - +
103A LEU* 3.8 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 4.2 23.7 - - + +
93A ASP* 3.8 13.0 + - - +
94A LEU* 1.3 77.0 - - - +
96A LYS* 1.3 56.1 + - - +
98A VAL* 3.2 9.2 + - - +
99A ASP* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 3.2 28.3 + - + +
94A LEU 3.3 0.4 - - - -
95A ALA* 1.3 77.6 - - - +
97A LEU* 1.3 57.1 + - - +
99A ASP* 3.5 6.5 + - - +
100A GLU* 3.0 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 5.9 4.0 - - + -
64A ILE* 4.6 14.6 - - + -
65A ILE* 5.8 6.1 - - + -
93A ASP 3.7 9.0 + - - +
94A LEU* 3.2 14.9 + - + +
96A LYS* 1.3 76.9 - - - +
98A VAL* 1.3 58.5 + - - +
100A GLU* 4.0 9.1 - - - -
101A GLY 3.3 1.4 + - - -
102A LYS* 3.0 32.0 + - + +
103A LEU* 3.0 24.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 4.8 13.5 - - + -
94A LEU* 2.9 21.7 + - + +
95A ALA* 3.2 10.7 + - - +
97A LEU* 1.3 73.9 - - - +
99A ASP* 1.3 60.9 + - - +
101A GLY* 2.8 25.1 + - - -
103A LEU* 3.4 31.7 - - + +
104A PHE* 5.7 4.0 - - + -
105A ILE* 5.0 13.2 - - + +
137A TYR* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA 3.0 16.1 + - - +
96A LYS* 3.8 7.0 - - - +
98A VAL* 1.3 77.5 - - - +
100A GLU* 1.3 62.1 + - + +
101A GLY* 3.3 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LYS* 3.0 29.9 + - - +
97A LEU* 4.1 3.8 - - - +
99A ASP* 1.3 76.1 - - + +
101A GLY* 1.3 61.0 + - - +
102A LYS* 3.4 33.2 + - + +
----------------------------------------------------------
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