Contacts of the helix formed by residues 74 - 84 (chain C) in PDB entry 4LXZ
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 SER 74 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 5.4 2.9 - - - -
332B GLU* 3.6 28.5 + - - -
70C THR* 4.5 0.2 - - - -
72C TYR 3.9 0.6 + - - -
73C HIS* 1.3 74.9 - - - +
75C ASP* 1.3 63.7 + - - +
76C GLU* 3.8 6.5 + - - +
77C TYR* 3.1 25.5 + - - +
78C ILE* 3.1 22.3 + - - +
99C PHE* 4.7 0.9 - - - -
149C LYS* 3.0 15.1 + - - +
150C SER* 3.6 14.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B PRO* 3.3 19.8 - - + +
331B ASN* 2.9 27.1 + - - +
332B GLU* 2.8 31.9 + - + +
406B PG4 5.6 2.8 - - - +
70C THR* 4.1 19.9 + - - +
73C HIS 3.8 0.7 + - - +
74C SER* 1.3 73.2 - - - +
76C GLU* 1.3 61.7 + - + +
78C ILE* 3.3 1.9 + - - +
79C LYS* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C SER* 3.3 6.1 + - - +
75C ASP* 1.3 81.0 - - + +
77C TYR* 1.4 58.1 + - - +
79C LYS* 3.8 17.3 - - - +
80C PHE* 3.0 28.6 + - - +
98C ARG* 6.2 0.2 - - - -
99C PHE* 3.8 19.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C HIS* 3.7 21.5 - + + -
74C SER* 3.1 22.2 + - - +
76C GLU* 1.4 74.3 - - - +
78C ILE* 1.3 60.4 + - + +
80C PHE* 3.3 3.6 + + - +
81C LEU* 3.0 52.2 + - + +
99C PHE* 3.5 44.8 - + + -
101C VAL* 4.7 0.4 - - + -
148C LYS 4.1 5.6 - - - -
149C LYS 3.5 15.5 - - - +
150C SER* 3.8 12.3 - - - -
151C GLU 3.9 1.6 - - - -
152C ALA* 3.3 31.7 + - + +
157C TYR* 2.6 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ALA* 3.8 38.6 - - + +
69C MET* 3.8 28.5 - - + -
70C THR* 4.0 13.0 - - + -
73C HIS* 3.6 31.0 - - + -
74C SER 3.1 17.3 + - - +
75C ASP 4.0 3.4 - - - +
77C TYR* 1.3 73.5 - - + +
79C LYS* 1.3 59.7 + - - +
81C LEU* 3.2 22.8 + - + +
82C ARG* 2.9 29.5 + - - +
112C PHE* 4.1 9.2 - - + -
158C VAL* 4.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ASP 2.8 19.1 + - - +
76C GLU* 3.8 20.2 - - - +
78C ILE* 1.3 76.6 - - - +
80C PHE* 1.3 54.8 + - - +
82C ARG* 3.3 10.3 + - + +
83C SER* 2.7 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLU 3.0 15.1 + - - +
77C TYR* 3.4 9.6 - + - +
79C LYS* 1.3 76.1 - - - +
81C LEU* 1.4 65.6 + - + +
83C SER* 3.0 5.1 + - - -
84C ILE* 2.8 67.1 + - + +
92C TYR* 3.9 17.7 - + + -
95C GLN* 3.6 28.5 - - + -
96C MET* 3.7 25.1 - - + -
99C PHE* 3.5 27.8 - + + -
101C VAL* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR* 3.0 54.2 + - + +
78C ILE* 3.2 14.3 + - + +
80C PHE* 1.4 85.7 - - + +
82C ARG* 1.3 59.6 + - - +
83C SER 3.5 0.2 + - - -
84C ILE* 3.9 14.9 + - - +
85C ARG* 4.8 0.5 + - - -
101C VAL* 4.5 4.3 - - + -
111C LEU* 4.3 16.4 - - + +
112C PHE* 3.7 28.1 + - + +
115C CYS* 4.9 2.9 - - - -
157C TYR* 4.1 25.1 - - + +
158C VAL* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ALA* 3.6 33.5 - - - +
67C GLU* 4.5 11.7 + - - -
78C ILE* 2.9 16.5 + - - +
79C LYS* 3.4 10.5 - - + +
80C PHE 3.2 0.2 - - - -
81C LEU* 1.3 75.9 - - - +
83C SER* 1.3 55.2 + - - +
85C ARG* 2.8 28.8 + - - -
112C PHE* 3.7 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LYS* 2.7 35.9 + - - +
80C PHE* 3.0 3.3 + - - -
82C ARG* 1.3 79.1 - - - +
84C ILE* 1.3 62.6 + - - +
85C ARG* 3.5 11.5 + - - +
88C ASN* 3.1 21.5 + - - -
92C TYR* 3.5 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PHE* 2.8 44.6 + - + +
81C LEU* 3.9 15.7 - - - +
83C SER* 1.3 72.1 - - - +
85C ARG* 1.3 71.9 + - - +
88C ASN* 3.5 16.4 - - - +
89C MET* 4.1 16.2 - - + -
92C TYR* 3.6 32.5 - - + -
96C MET* 4.5 2.9 - - - -
101C VAL* 5.0 0.2 - - + -
107C VAL* 3.6 27.8 - - + +
108C PHE 5.4 2.6 - - - +
111C LEU* 4.0 25.4 - - + +
----------------------------------------------------------
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