Contacts of the helix formed by residues 112 - 127 (chain W) 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 W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75W ILE* 4.0 15.9 - - + -
110W LEU 3.3 9.9 - - - +
111W ASN* 1.3 93.2 - - - +
113W LYS* 1.3 56.9 + - - +
114W ALA* 3.0 7.4 - - + +
115W ASN* 2.8 47.5 + - - +
116W ARG* 3.5 3.8 + - - +
195X GLU* 5.3 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111W ASN 3.4 4.7 + - - -
112W PRO* 1.3 69.2 - - - +
114W ALA* 1.3 56.6 + - - +
116W ARG* 3.4 4.1 + - - +
117W GLU* 3.1 35.9 + - - +
371W HIS* 3.2 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112W PRO* 2.9 5.1 + - + +
113W LYS* 1.3 78.2 - - - +
115W ASN* 1.3 63.2 + - - +
117W GLU* 3.7 13.7 - - - +
118W LYS* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75W ILE* 3.5 24.5 - - - +
76W ILE* 3.8 16.3 + - + +
79W TRP* 3.6 27.9 - - + -
111W ASN* 3.3 25.5 + - - +
112W PRO* 2.8 27.1 + - - +
114W ALA* 1.3 73.5 - - - +
116W ARG* 1.4 57.6 + - - +
118W LYS* 2.8 3.2 + - - +
119W MET* 2.8 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107W GLU* 3.1 41.6 + - - +
111W ASN* 4.1 1.7 - - - +
112W PRO 3.5 3.8 + - - +
113W LYS* 3.4 11.5 + - - +
115W ASN* 1.4 76.1 - - - +
117W GLU* 1.3 56.1 + - - +
119W MET* 3.4 11.8 - - - +
120W THR* 2.6 33.2 + - - +
134W VAL* 3.2 40.2 + - + +
135W ALA* 4.9 0.2 - - - +
136W ILE* 4.0 20.6 - - - +
370W VAL* 3.5 20.4 + - + +
371W HIS* 3.7 35.9 + - - +
372W ARG* 3.6 32.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113W LYS* 3.1 21.8 + - - +
114W ALA* 3.7 13.2 - - - +
116W ARG* 1.3 76.8 - - - +
118W LYS* 1.3 56.0 + - - +
120W THR* 3.4 5.0 + - - -
121W GLN* 3.0 27.0 + - - +
367W PRO* 3.6 26.8 - - + +
368W SER* 3.9 18.9 + - - -
370W VAL* 5.2 0.2 - - - -
371W HIS* 3.7 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79W TRP* 3.8 45.2 - - + +
114W ALA 3.0 16.1 + - - +
115W ASN* 2.8 15.1 + - - +
117W GLU* 1.3 70.5 - - - +
119W MET* 1.3 56.2 + - - +
120W THR 3.0 0.2 - - - -
121W GLN* 3.1 37.1 + - + +
122W ILE* 3.0 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 119 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W ASN* 4.8 2.7 - - - +
76W ILE* 4.5 14.8 - - + -
79W TRP* 3.8 10.6 - - + -
86W TRP* 3.9 26.0 - - + -
105W LEU* 3.7 29.2 - - + -
106W THR 4.1 19.5 - - - +
107W GLU* 5.0 0.4 - - - -
111W ASN* 4.5 11.4 - - - -
115W ASN 2.8 20.1 + - - +
116W ARG* 3.4 20.2 - - - +
118W LYS* 1.3 71.4 - - - +
120W THR* 1.3 62.1 + - - +
122W ILE* 3.8 7.5 - - - +
123W MET* 2.9 35.0 + - - +
132W MET* 4.5 0.2 - - - -
134W VAL* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116W ARG 2.6 23.0 + - - -
117W GLU* 3.4 5.8 - - - -
119W MET* 1.3 78.0 - - - +
121W GLN* 1.3 66.6 + - - +
124W PHE* 2.9 51.7 + - + +
132W MET* 3.8 18.1 - - - +
134W VAL* 4.5 1.6 - - - +
362W TYR* 4.3 13.7 - - + -
367W PRO* 4.6 2.0 - - + +
370W VAL* 3.2 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117W GLU 3.0 14.3 + - - +
118W LYS* 3.1 44.9 + - + +
120W THR* 1.3 74.7 - - - +
122W ILE* 1.3 63.5 + - - +
125W GLU* 2.8 65.1 + - - +
126W THR* 4.9 6.9 - - - +
362W TYR* 3.6 17.7 + - - +
367W PRO* 4.7 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79W TRP* 3.6 42.6 - - + +
83W GLU* 4.1 17.3 - - + +
86W TRP* 4.1 14.8 - - + -
118W LYS* 3.0 30.6 + - - +
119W MET* 4.1 5.2 - - - +
121W GLN* 1.3 89.4 - - - +
123W MET* 1.3 68.6 + - - +
126W THR* 2.9 43.0 + - + +
127W PHE* 3.2 19.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 123 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86W TRP* 3.3 55.4 - - + +
90W PHE* 4.1 17.7 - - + -
103W THR* 4.6 8.5 - - - -
105W LEU* 3.7 15.5 - - + -
119W MET 2.9 23.6 + - - +
120W THR 3.2 1.5 + - - +
122W ILE* 1.3 79.1 - - - +
124W PHE* 1.3 57.6 + - - +
127W PHE* 3.2 24.5 + - + +
128W ASN 3.0 21.7 + - - -
129W VAL* 3.6 20.7 + - + -
132W MET* 3.6 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120W THR* 2.9 27.8 + - + +
123W MET* 1.3 78.2 - - - +
125W GLU* 1.3 57.7 + - - +
128W ASN* 3.3 23.0 - - - +
129W VAL* 3.5 27.4 - - + +
130W PRO 3.7 10.5 - - - -
131W ALA* 3.8 5.2 - - - -
132W MET* 3.4 26.2 - - + -
357W ILE* 3.0 48.9 - - + -
358W THR 4.0 2.7 - - - -
359W LYS* 3.8 14.4 - - + -
362W TYR* 3.6 38.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121W GLN* 2.8 49.5 + - - +
124W PHE* 1.3 75.2 - - - +
126W THR* 1.4 59.7 + - + +
128W ASN* 4.7 1.8 - - - +
362W TYR* 3.5 33.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 126 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83W GLU* 4.2 26.1 + - - +
121W GLN* 4.9 9.6 - - - +
122W ILE* 2.9 37.5 + - + +
125W GLU* 1.4 79.0 - - + +
127W PHE* 1.3 72.0 + - - +
128W ASN* 3.6 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83W GLU* 3.7 20.9 - - + -
86W TRP* 3.6 31.4 - + + -
87W HIS* 4.0 20.6 - - + -
90W PHE* 3.6 30.7 - + + -
91W TYR* 4.9 7.0 - + - -
98W PRO* 3.7 19.0 - - + +
99W GLU* 3.5 13.5 + - - +
122W ILE* 3.4 36.1 - - + -
123W MET* 3.2 28.1 + - + +
126W THR* 1.3 82.5 + - - +
128W ASN* 1.3 74.0 + - - +
129W VAL* 3.4 8.4 + - + -
----------------------------------------------------------
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