Contacts of the helix formed by residues 112 - 127 (chain X) in PDB entry 1O1F
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 X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75X ILE* 3.9 17.0 - - + -
110X LEU 3.3 9.9 - - - +
111X ASN* 1.3 93.7 + - - +
113X LYS* 1.3 57.2 + - - +
114X ALA* 3.0 5.6 - - + +
115X ASN* 2.8 47.8 + - - +
116X ARG* 3.5 4.0 + - - +
195Y GLU* 5.3 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111X ASN 3.4 4.8 + - - -
112X PRO* 1.3 69.6 - - - +
114X ALA* 1.3 55.7 + - - +
116X ARG* 3.4 3.8 + - - -
117X GLU* 3.1 36.0 + - - +
371X HIS* 3.2 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112X PRO* 2.9 4.9 + - + +
113X LYS* 1.3 78.6 - - - +
115X ASN* 1.3 62.7 + - - +
117X GLU* 3.7 14.7 - - - +
118X LYS* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75X ILE* 3.5 23.2 - - - +
76X ILE* 3.8 17.1 + - + +
79X TRP* 3.6 27.7 + - + -
111X ASN* 3.3 25.3 + - - +
112X PRO* 2.8 27.1 + - - +
114X ALA* 1.3 70.8 - - - +
116X ARG* 1.4 57.9 + - - +
117X GLU 3.2 0.2 - - - -
118X LYS* 2.8 3.0 + - - +
119X MET* 2.8 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107X GLU* 3.1 42.4 + - - +
111X ASN* 4.1 2.4 - - - +
112X PRO 3.5 3.4 + - - +
113X LYS* 3.4 11.5 + - - +
115X ASN* 1.4 77.0 - - - +
117X GLU* 1.3 56.7 + - - +
119X MET* 3.4 12.4 - - - +
120X THR* 2.6 33.2 + - - +
134X VAL* 3.2 39.8 + - + +
136X ILE* 4.0 20.6 - - - +
370X VAL* 3.5 20.5 + - + +
371X HIS* 3.7 37.5 + - - +
372X ARG* 3.6 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113X LYS* 3.1 20.8 + - - +
114X ALA* 3.7 12.4 - - - +
116X ARG* 1.3 76.8 - - - +
118X LYS* 1.3 55.5 + - - +
120X THR* 3.4 5.1 + - - -
121X GLN* 3.0 26.7 + - - +
367X PRO* 3.6 27.1 - - + +
368X SER* 3.9 18.6 + - - -
371X HIS* 3.7 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79X TRP* 3.8 45.1 - - + +
114X ALA 3.0 16.8 + - - +
115X ASN 2.8 13.2 + - - +
117X GLU* 1.3 71.3 - - - +
119X MET* 1.3 56.7 + - - +
121X GLN* 3.1 35.9 + - + +
122X ILE* 3.0 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 119 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X ASN* 4.8 2.5 - - - +
76X ILE* 4.5 14.6 - - + -
79X TRP* 3.8 9.7 - - + -
86X TRP* 3.9 26.7 - - + -
105X LEU* 3.7 29.6 - - + -
106X THR 4.1 20.2 - - - +
107X GLU* 5.0 0.9 - - + -
111X ASN* 4.5 11.2 - - - -
115X ASN 2.8 20.5 + - - +
116X ARG* 3.4 20.6 - - - +
118X LYS* 1.3 71.7 - - - +
120X THR* 1.3 62.0 + - - +
122X ILE* 3.8 7.5 - - - +
123X MET* 2.9 35.7 + - - +
132X MET* 4.5 0.2 - - - -
134X VAL* 4.3 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116X ARG 2.6 22.3 + - - -
117X GLU* 3.4 5.8 + - - -
118X LYS 3.0 0.2 - - - -
119X MET* 1.3 78.4 - - - +
121X GLN* 1.3 64.5 + - - +
123X MET* 3.8 0.2 - - - +
124X PHE* 2.9 51.7 + - + +
132X MET* 3.8 17.4 - - - +
134X VAL* 4.5 2.1 - - - +
362X TYR* 4.3 14.6 - - + -
367X PRO* 4.6 2.0 - - + +
370X VAL* 3.2 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117X GLU 3.0 14.5 + - - +
118X LYS* 3.1 46.3 + - + +
120X THR* 1.3 75.0 - - - +
122X ILE* 1.3 63.8 + - - +
125X GLU* 2.8 64.2 + - - +
126X THR* 4.9 7.1 - - - +
362X TYR* 3.6 17.7 + - - +
367X PRO* 4.7 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79X TRP* 3.6 42.6 - - + +
83X GLU* 4.1 18.4 - - + +
86X TRP* 4.1 15.3 - - + -
118X LYS* 3.0 29.3 + - - +
119X MET* 4.1 4.9 - - - +
121X GLN* 1.3 90.1 - - - +
123X MET* 1.3 68.5 + - - +
126X THR* 2.9 42.6 + - + +
127X PHE* 3.2 19.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 123 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86X TRP* 3.3 55.0 - - + +
90X PHE* 4.1 16.8 - - + -
103X THR* 4.6 8.7 - - - -
105X LEU* 3.7 15.0 - - + -
119X MET 2.9 23.8 + - - +
120X THR 3.2 2.0 + - - +
122X ILE* 1.3 79.3 - - - +
124X PHE* 1.3 57.5 + - - +
127X PHE* 3.2 24.8 + - + +
128X ASN 3.0 21.5 + - - -
129X VAL* 3.6 20.7 + - + -
132X MET* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120X THR* 2.9 27.8 + - + +
123X MET* 1.3 78.5 - - - +
125X GLU* 1.3 59.4 + - - +
128X ASN* 3.3 23.0 - - - +
129X VAL* 3.5 26.7 - - + +
130X PRO 3.7 11.0 - - - -
131X ALA* 3.8 4.9 - - - -
132X MET* 3.4 26.5 - - + -
357X ILE* 3.0 48.0 - - + -
358X THR 4.0 2.7 - - - -
359X LYS* 3.8 14.8 - - + -
362X TYR* 3.6 37.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121X GLN* 2.8 49.0 + - - +
124X PHE* 1.3 76.0 - - - +
126X THR* 1.3 59.3 + - + +
128X ASN* 4.7 2.3 - - - +
362X TYR* 3.5 33.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 126 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X GLU* 4.2 26.3 + - - +
121X GLN* 4.9 10.1 - - - +
122X ILE* 2.9 37.5 + - + +
125X GLU* 1.3 77.9 - - + +
127X PHE* 1.3 73.3 + - - +
128X ASN* 3.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X GLU* 3.7 21.3 - - + -
86X TRP* 3.6 32.1 - + + -
87X HIS* 4.0 20.0 - - + -
90X PHE* 3.6 30.5 - + + -
91X TYR* 4.9 7.6 + + - -
98X PRO* 3.6 18.9 - - + +
99X GLU* 3.5 13.0 - - - +
122X ILE* 3.4 37.5 - - + -
123X MET* 3.2 28.7 + - + +
126X THR* 1.3 81.0 + - - +
128X ASN* 1.3 73.7 + - - +
129X VAL* 3.4 9.1 + - + -
----------------------------------------------------------
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