Contacts of the helix formed by residues 89 - 96 (chain C) in PDB entry 4QLC
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 89 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLU* 5.4 3.7 - - - +
64C LEU* 3.7 26.1 - - + +
85C ALA 3.4 15.1 + - - +
86C ILE 3.0 6.5 + - - +
87C ARG 4.9 0.2 - - - -
88C ASN* 1.3 75.9 - - - +
90C GLU* 1.3 67.7 + - - +
91C GLU* 3.6 10.4 + - - +
92C LEU* 3.0 31.9 + - + +
93C ASN* 2.8 23.4 + - - +
103D LEU* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG 5.8 0.2 - - - -
88C ASN 3.6 5.5 + - - -
89C ASP* 1.3 71.5 - - - +
91C GLU* 1.3 74.9 + - + +
93C ASN* 3.7 6.9 + - - +
94C LYS* 3.3 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ASP* 3.2 9.8 + - - +
90C GLU* 1.3 90.9 - - + +
92C LEU* 1.3 64.1 + - - +
94C LYS* 3.3 15.9 + - - +
95C LEU* 3.1 21.7 + - - +
100D PRO* 2.7 41.1 - - - +
101D GLY* 4.3 2.9 - - - -
102D GLU* 3.8 25.0 + - + +
103D LEU* 3.7 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 5.0 4.5 - - + -
60C GLU* 4.4 11.4 - - + -
61C VAL* 3.8 35.2 - - + -
64C LEU* 3.5 31.4 - - + -
85C ALA 5.3 0.2 - - - -
86C ILE* 3.9 23.6 - - + +
89C ASP* 3.0 15.2 + - + +
91C GLU* 1.3 75.9 - - - +
93C ASN* 1.3 60.7 + - - +
95C LEU* 3.3 25.9 + - + +
96C LEU* 2.9 37.6 + - + +
62D PHE* 5.5 1.1 - - + -
103D LEU* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A CIT 4.0 34.4 + - - +
86C ILE* 3.5 14.7 + - - +
87C ARG* 3.1 47.3 + - - +
89C ASP 2.8 16.4 + - - +
90C GLU* 3.7 7.7 + - - +
92C LEU* 1.3 76.5 - - - +
94C LYS* 1.3 63.4 + - - +
96C LEU 3.2 3.1 - - - -
97C SER* 3.0 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 6.5 1.3 - - + -
90C GLU* 3.3 24.7 + - - +
91C GLU* 3.6 18.9 + - - +
92C LEU 3.3 0.4 - - - -
93C ASN* 1.3 79.4 - - - +
95C LEU* 1.3 61.4 + - - +
97C SER* 3.0 28.2 + - - +
100D PRO* 3.5 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 4.1 21.8 - - + -
91C GLU 3.1 13.0 + - - +
92C LEU* 3.3 30.0 + - + +
94C LYS* 1.3 77.7 - - - +
96C LEU* 1.3 69.0 + - + +
97C SER* 3.5 1.6 + - - -
62D PHE* 4.8 7.2 - - + -
66D ILE* 4.7 7.6 - - + -
69D ARG* 3.6 39.4 + - - +
98D LEU* 4.3 4.9 - - + +
99D LEU* 4.7 9.6 - - + -
100D PRO* 3.9 24.6 - - + +
103D LEU* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL* 5.4 2.2 - - + -
86C ILE* 3.6 38.4 - - + -
87C ARG* 2.6 34.7 + - - +
92C LEU* 2.9 20.5 + - + +
93C ASN 3.2 4.3 - - - -
95C LEU* 1.3 91.5 - - + +
97C SER* 1.3 57.9 - - - +
98C GLY 3.2 3.7 + - - +
99C VAL* 3.5 28.9 - - + +
101C ILE* 5.5 0.2 - - + -
62D PHE* 3.8 38.1 - - + -
66D ILE* 5.4 0.9 - - + -
69D ARG* 5.0 6.5 - - - +
98F TYR* 4.3 10.5 - - + +
----------------------------------------------------------
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