Contacts of the helix formed by residues 112 - 128 (chain F) in PDB entry 3LUE
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 PRO 112 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E GLY* 6.5 1.8 - - - -
73F HIS* 3.9 13.0 - - + -
75F ILE* 3.8 17.7 - - + -
110F LEU 3.6 2.0 - - - +
111F ASN* 1.3 95.7 - - - +
113F LYS* 1.3 64.5 + - - +
114F ALA* 3.4 2.2 - - + +
115F ASN* 3.0 33.7 + - - +
116F ARG* 3.3 5.9 + - - +
177F ARG* 3.3 13.7 - - - +
179F ASP* 5.0 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E GLU 3.5 9.4 + - - +
196E ARG* 3.1 50.7 - - + +
197E GLY* 5.2 1.1 - - - +
111F ASN 3.5 2.5 + - - -
112F PRO* 1.3 70.2 - - - +
114F ALA* 1.3 63.5 + - + +
116F ARG* 3.2 20.5 + - - +
117F GLU* 3.2 18.4 + - - +
177F ARG* 4.8 0.4 - - - +
371F HIS* 3.5 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F PRO* 3.4 2.3 - - + +
113F LYS* 1.3 76.2 - - + +
115F ASN* 1.3 64.3 + - - +
117F GLU* 3.8 12.0 - - - +
118F LYS* 2.8 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ILE* 3.3 28.3 - - - +
76F VAL* 3.5 18.8 + - - +
79F TRP* 4.1 21.0 - - + +
111F ASN* 3.2 24.4 + - - +
112F PRO* 3.0 22.7 + - - +
114F ALA* 1.3 77.3 + - - +
116F ARG* 1.3 65.3 + - - +
118F LYS* 3.0 3.2 + - - +
119F MET* 2.9 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F GLU* 3.0 51.8 + - - +
111F ASN* 3.5 24.0 - - - +
112F PRO 3.8 4.3 - - - +
113F LYS* 3.2 12.5 + - - +
115F ASN* 1.3 75.4 - - - +
117F GLU* 1.3 60.4 + - - +
119F MET* 3.4 13.7 + - + +
120F THR* 2.9 27.7 + - - -
134F VAL* 4.4 8.8 + - + +
370F VAL* 3.2 35.1 + - + +
371F HIS* 3.8 21.1 + - + +
374F CYS* 3.0 37.2 + - - +
375F PHE* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F LYS* 3.4 15.9 - - - +
114F ALA* 3.8 10.7 - - - +
115F ASN 3.2 0.6 - - - -
116F ARG* 1.3 73.8 - - - +
118F LYS* 1.3 65.8 + - - +
120F THR* 2.9 3.5 + - - -
121F GLN* 2.9 26.5 + - - +
367F PRO* 3.9 30.1 - - + +
368F SER* 4.2 14.2 + - - -
370F VAL* 4.0 7.6 - - - -
371F HIS* 2.8 31.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F TRP* 3.4 53.4 - - + +
80F ASP* 5.8 0.6 + - - -
83F GLU* 4.5 6.3 + - - -
114F ALA 2.8 22.6 + - - +
115F ASN 3.0 3.7 + - - +
117F GLU* 1.3 71.3 - - - +
119F MET* 1.3 57.8 + - - +
121F GLN* 3.1 16.7 - - + +
122F ILE* 3.0 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ASN* 5.7 0.4 - - - -
76F VAL* 6.4 1.8 - - + -
79F TRP* 4.2 13.6 - - + -
86F TRP* 4.2 22.0 - - + -
105F LEU* 3.5 27.4 - - + -
106F THR 4.7 5.2 - - - +
107F GLU* 4.4 7.6 - - + -
111F ASN* 3.5 28.3 - - - +
115F ASN* 2.9 19.5 + - + +
116F ARG* 3.5 11.2 - - - +
118F LYS* 1.3 76.9 - - - +
120F THR* 1.4 60.5 + - - +
122F ILE* 4.7 3.1 - - - -
123F MET* 3.2 31.0 + - - +
132F MET* 3.9 0.8 - - - +
134F VAL* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F ARG 2.9 14.8 + - - -
117F GLU 2.9 7.9 + - - -
119F MET* 1.4 75.1 - - - +
121F GLN* 1.3 59.8 + - - +
123F MET* 3.6 0.7 + - - +
124F PHE* 2.9 49.6 + - + -
132F MET* 4.1 15.3 - - - -
357F ILE* 5.3 2.0 - - + -
362F TYR* 3.7 25.6 - - + -
367F PRO* 4.2 10.8 - - + +
369F ILE* 4.9 6.5 - - + -
370F VAL* 3.0 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F GLU* 2.9 13.4 + - - +
118F LYS* 3.1 24.9 - - + +
120F THR* 1.3 76.6 - - - +
122F ILE* 1.4 56.7 + - + +
124F PHE* 3.7 0.3 - - - -
125F GLU* 2.9 70.6 + - - +
362F TYR* 3.3 17.0 + - - -
367F PRO* 3.9 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F TRP* 3.5 36.1 - - + -
83F GLU* 3.9 30.1 - - + +
86F TRP* 4.0 15.7 - - + -
118F LYS* 3.0 33.4 + - + +
119F MET* 4.4 3.6 - - - +
121F GLN* 1.4 75.4 - - + +
123F MET* 1.3 69.4 + - - +
126F THR* 2.8 38.3 + - - +
127F PHE* 2.9 32.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F TRP* 3.5 42.6 - - + -
90F PHE* 4.0 16.6 - - + -
103F VAL* 3.8 22.9 - - - -
105F LEU* 3.8 15.3 - - + -
119F MET 3.2 20.6 + - - +
120F THR 3.9 1.6 - - - +
122F ILE* 1.3 82.2 - - + +
124F PHE* 1.3 58.6 + - - +
127F PHE* 3.1 37.3 + - + +
128F ASN 3.2 3.5 + - - -
129F THR* 2.7 27.3 + - - +
132F MET* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F THR* 2.9 35.7 + - + +
123F MET* 1.3 76.1 - - - +
125F GLU* 1.3 59.1 + - - +
128F ASN* 3.0 26.7 - - - +
129F THR* 3.0 31.9 - - - +
131F ALA* 4.0 5.6 - - - -
132F MET* 3.6 25.4 - - + -
357F ILE* 3.6 28.5 - - + -
358F SER 4.0 6.7 - - - -
359F LYS* 3.7 35.8 + - + +
362F TYR* 3.3 45.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F GLN* 2.9 41.0 + - - +
124F PHE* 1.3 71.9 - - - +
126F THR* 1.4 66.8 + - - +
128F ASN* 4.4 5.0 + - - +
359F LYS* 4.7 6.5 - - - +
362F TYR* 2.8 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F GLU* 3.9 23.4 + - - +
122F ILE* 2.8 34.8 + - + +
125F GLU* 1.4 76.4 - - - +
127F PHE* 1.3 78.8 + - + +
128F ASN* 5.3 0.4 - - - +
120Q LYS* 6.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F TYR 5.8 0.4 - - - -
83F GLU* 4.0 11.9 - - + -
86F TRP* 3.9 16.6 - + + -
87F HIS* 3.7 42.2 - - + -
90F PHE* 4.2 6.7 - + + -
91F TYR* 4.1 23.5 + + - -
98F PRO* 3.3 32.4 - - + +
99F GLU* 3.8 6.2 - - - +
122F ILE* 2.9 34.0 + - + -
123F MET* 3.4 26.7 - - + +
126F THR* 1.3 89.1 - - + +
128F ASN* 1.3 72.6 + - - +
129F THR* 3.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F GLU* 3.1 39.0 + - + +
123F MET 3.2 0.6 + - - -
124F PHE 3.0 18.1 + - - +
125F GLU 4.3 4.5 - - - +
126F THR 3.6 1.8 - - - -
127F PHE* 1.3 81.2 - - - +
129F THR* 1.3 62.4 + - - +
130F PRO 3.9 0.2 - - - -
359F LYS* 3.8 20.8 + - - +
----------------------------------------------------------
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