Contacts of the helix formed by residues 96 - 108 (chain F) in PDB entry 4CQM
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 LYS 96 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F ARG* 3.6 24.8 + - - +
95F THR* 1.3 77.3 - - - +
97F THR* 1.3 61.0 + - + +
98F GLU* 4.4 5.6 - - + +
99F ASP* 3.0 44.0 + - - +
100F MET* 3.1 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F THR 3.7 1.6 + - - -
96F LYS* 1.3 73.9 - - + +
98F GLU* 1.3 77.7 + - + +
100F MET* 3.2 18.9 + - - +
101F VAL* 3.0 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F LYS* 3.2 4.1 - - + +
97F THR* 1.3 95.4 + - + +
99F ASP* 1.3 65.6 + - - +
100F MET 3.2 0.2 - - - -
101F VAL* 3.9 16.3 - - - +
102F SER* 3.0 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F ARG* 5.6 7.2 - - + -
95F THR* 4.5 7.6 - - + -
96F LYS* 3.0 40.0 + - + +
98F GLU* 1.3 79.9 - - - +
100F MET* 1.3 63.8 + - - +
102F SER* 3.6 9.0 - - - -
103F GLN* 3.5 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F LEU* 3.7 32.3 - - + +
95F THR* 3.3 38.8 - - + +
96F LYS 3.1 9.5 + - - +
97F THR* 3.2 19.5 + - - +
99F ASP* 1.3 76.7 - - - +
101F VAL* 1.3 66.2 + - + +
102F SER 3.3 0.2 + - - -
103F GLN 3.4 1.7 + - - -
104F LEU* 3.1 36.0 + - + +
147F VAL* 3.9 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F THR* 3.0 24.2 + - - +
98F GLU* 4.0 19.3 - - - +
100F MET* 1.3 75.9 - - + +
102F SER* 1.3 62.7 + - - +
104F LEU* 4.4 9.0 - - + -
105F HIS* 3.1 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ILE* 3.4 18.9 - - - +
98F GLU 3.0 20.6 + - - -
99F ASP* 3.6 13.7 - - - -
100F MET 3.1 0.2 - - - -
101F VAL* 1.3 78.5 - - - +
103F GLN* 1.3 58.6 + - - +
105F HIS* 3.9 2.8 - - - +
106F THR* 2.9 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ILE* 3.7 29.7 - - + +
88F ARG* 3.3 44.2 + - + +
95F THR* 5.6 1.2 - - - +
99F ASP* 3.5 16.2 + - - +
100F MET 3.4 3.8 + - - +
102F SER* 1.3 74.4 - - - +
104F LEU* 1.3 59.1 + - - +
106F THR* 4.4 0.2 - - - -
107F ASN* 2.7 44.9 + - - +
147F VAL* 3.3 28.9 - - + +
148F TYR* 3.6 23.9 - - - +
151F SER* 3.8 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F MET* 3.1 31.0 + - + +
101F VAL* 4.1 7.2 - - + +
103F GLN* 1.3 77.3 - - - +
105F HIS* 1.3 65.7 + - + +
108F LEU* 3.2 19.2 - - + +
109F LEU* 3.0 23.9 + - - +
147F VAL* 4.4 7.2 - - + +
150F ALA* 4.3 15.3 - - + +
151F SER* 3.6 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F ALA* 4.1 23.4 + - + +
101F VAL* 3.1 45.7 + - + +
102F SER* 3.9 3.1 - - - +
104F LEU* 1.3 87.0 - - + +
106F THR* 1.3 56.2 + - - +
109F LEU* 3.4 29.1 - - + +
110F GLY* 2.6 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F ARG* 5.6 5.0 + - - +
56F ASP* 5.4 2.2 + - - +
57F VAL* 3.6 28.7 - - + +
58F ALA* 4.6 10.1 - - - +
84F ALA* 3.8 7.8 - - + +
85F GLY* 3.9 14.4 - - - +
86F ILE* 3.6 27.2 - - + +
102F SER* 2.9 22.6 + - - -
103F GLN 3.9 0.9 - - - -
105F HIS* 1.3 79.9 - - - +
107F ASN* 1.3 74.4 + - - +
110F GLY* 3.7 5.2 - - - -
111F SER* 4.3 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ALA 4.5 3.7 - - - +
85F GLY* 3.2 6.1 - - - -
86F ILE* 2.9 44.8 + - - +
103F GLN* 2.7 30.8 + - - +
106F THR* 1.3 76.2 - - - +
108F LEU* 1.3 58.0 + - - +
111F SER* 3.4 18.9 + - - -
148F TYR* 3.9 11.9 - - - -
151F SER* 3.6 26.4 + - - -
152F LYS* 3.4 23.0 + - - +
155F LEU* 3.6 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F LEU* 3.2 22.2 + - + +
107F ASN* 1.3 78.6 - - - +
109F LEU* 1.3 67.5 + - - +
110F GLY 3.2 1.3 - - - -
111F SER* 3.2 6.4 + - - -
112F MET* 3.1 40.9 + - + +
150F ALA 4.4 6.7 - - - +
151F SER* 3.7 17.0 - - - +
154F GLY* 3.5 42.2 - - - +
155F LEU* 3.5 12.8 - - + +
158F PHE* 5.0 1.3 - - + -
----------------------------------------------------------
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