Contacts of the helix formed by residues 105 - 123 (chain F) in PDB entry 4KYI
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 ASN 105 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ASP* 2.9 18.4 + - - +
103F ILE 3.1 4.6 + - - -
104F THR* 1.3 82.8 + - - +
106F THR* 1.3 60.4 + - - +
107F ASP* 2.9 40.6 + - - +
108F THR* 2.6 49.2 + - + +
109F PHE 3.8 1.2 + - - -
143F ALA* 4.2 1.1 - - - +
144F VAL* 4.4 1.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
105F ASN* 1.3 72.2 + - - +
107F ASP* 1.3 65.4 + - - +
109F PHE* 3.1 9.0 + - + +
110F ALA* 3.0 26.4 + - + +
143F ALA* 3.7 24.2 + - - +
144F VAL* 4.1 17.3 - - + -
148F GLU* 5.0 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F ASN* 2.9 18.7 + - - +
106F THR* 1.3 82.9 - - - +
108F THR* 1.3 50.9 + - + +
110F ALA* 3.2 8.9 + - - +
111F ARG* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLU* 4.1 19.7 + - + +
30F SER 5.2 1.1 - - - +
32F VAL* 4.0 22.0 - - + -
100F VAL 4.8 1.8 - - - +
101F TYR* 3.5 5.5 - - - +
102F ASP* 2.9 29.3 + - + -
105F ASN* 2.6 45.8 + - + +
107F ASP* 1.3 75.5 - - + +
109F PHE* 1.3 55.3 - - - +
111F ARG* 3.4 9.9 + - - +
112F ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F TYR* 3.6 42.6 - + + -
105F ASN 4.5 0.2 - - - +
106F THR* 3.1 13.1 + - + +
108F THR* 1.3 78.4 + - - +
110F ALA* 1.3 65.8 + - - +
112F ALA* 3.3 10.6 + - + +
113F LYS* 3.3 50.3 + - + +
131F LEU* 4.3 12.3 - - + -
144F VAL* 4.1 18.2 - - + -
148F GLU* 4.0 33.0 - - + -
149F ALA* 3.9 34.1 - - + -
152F TYR* 4.7 7.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F THR* 3.0 13.5 + - + +
107F ASP* 3.2 12.8 + - - +
109F PHE* 1.3 74.6 - - - +
111F ARG* 1.3 63.1 + - - +
112F ALA 3.5 0.2 + - - -
113F LYS* 3.6 19.1 + - + +
114F ASN* 3.0 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F GLY* 5.4 0.2 - - - -
29F GLU* 3.6 33.5 + - + +
84F HIS* 3.7 24.4 + - - +
107F ASP 2.7 17.2 + - - +
108F THR* 3.4 12.1 - - - +
109F PHE 3.2 0.2 - - - -
110F ALA* 1.3 77.0 - - - +
112F ALA* 1.3 61.8 + - - +
114F ASN* 3.3 31.9 + - - +
115F TRP* 3.1 68.8 + - + +
118F GLU* 5.6 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F GLY* 6.0 0.7 - - - -
99F VAL* 3.6 26.0 - - + +
100F VAL 5.1 0.4 - - - +
101F TYR* 4.0 14.8 - - + -
108F THR 2.9 14.8 + - - +
109F PHE* 3.4 14.6 - - + +
110F ALA 3.2 0.2 - - - -
111F ARG* 1.3 75.8 - - - +
113F LYS* 1.3 59.1 + - - +
115F TRP* 3.0 5.7 + - - +
116F VAL* 2.8 34.7 + - + +
131F LEU* 4.5 10.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
109F PHE* 3.3 48.9 + - + +
110F ALA* 3.8 14.3 - - + +
112F ALA* 1.3 76.4 - - - +
114F ASN* 1.3 61.6 + - - +
116F VAL* 3.5 2.1 + - - -
117F LYS* 2.8 29.8 + - - +
148F GLU* 5.1 4.9 + - - +
152F TYR* 3.5 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F ALA* 3.0 21.6 + - - +
111F ARG* 3.5 32.7 - - - +
112F ALA 3.1 1.0 - - - -
113F LYS* 1.3 79.2 - - - +
115F TRP* 1.3 59.1 - - - +
117F LYS* 3.7 9.9 - - - +
118F GLU* 2.9 30.8 + - - +
121F ARG* 4.6 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F LEU* 3.6 32.1 - - + -
28F GLY* 3.7 38.5 - - - -
79F GLY* 5.8 4.7 - - - -
83F TYR 5.5 0.9 - - - -
84F HIS* 4.0 19.5 - + - -
87F ALA* 3.8 30.7 - - + -
91F TYR* 4.8 1.6 - + - -
99F VAL* 4.1 15.3 - - + -
111F ARG* 3.1 63.6 + - + +
112F ALA* 3.0 10.4 + - - +
114F ASN* 1.3 74.1 - - - +
116F VAL* 1.3 55.0 + - - +
118F GLU* 3.0 24.1 + - - +
119F LEU* 2.6 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F VAL* 4.2 18.4 - - + -
112F ALA* 2.8 25.4 + - + +
113F LYS* 3.6 6.5 - - - +
115F TRP* 1.3 72.2 - - - +
117F LYS* 1.3 58.9 + - - +
119F LEU* 3.2 10.3 + - - +
120F GLN* 2.8 56.0 + - + +
129F ILE* 4.6 8.5 - - + -
130F ALA 5.7 0.2 - - - +
131F LEU* 5.3 4.0 - - + -
152F TYR* 3.7 17.9 - - + +
156F ASN* 4.8 0.2 - - + -
158F LEU* 4.0 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F LYS 2.8 21.9 + - - +
114F ASN* 3.7 10.1 - - - +
116F VAL* 1.3 74.6 - - - +
118F GLU* 1.3 58.7 + - - +
120F GLN* 3.5 11.3 + - - +
121F ARG* 3.0 55.0 + - + +
152F TYR* 5.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F HIS* 3.4 28.8 + - - +
87F ALA* 4.8 3.1 - - - +
88F PRO* 4.9 4.0 - - - +
91F TYR* 3.0 28.3 + - + +
111F ARG* 5.6 2.1 + - - -
114F ASN 2.9 18.9 + - - +
115F TRP* 3.0 25.2 + - + +
117F LYS* 1.3 74.1 - - - +
119F LEU* 1.3 59.5 + - + +
121F ARG* 3.5 21.8 + - - +
122F GLN* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F LEU* 4.0 18.2 - - + -
91F TYR* 3.9 34.3 - - + -
97F ALA* 4.1 14.8 - - + -
99F VAL* 3.7 29.8 - - + -
115F TRP* 2.6 22.8 + - + +
116F VAL* 3.4 5.8 - - - +
118F GLU* 1.3 73.6 - - - +
120F GLN* 1.3 57.9 + - - +
123F ALA* 3.1 42.3 + - + +
124F SER 5.0 1.4 - - - +
127F ILE* 4.6 5.4 - - + +
129F ILE* 3.7 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F VAL* 2.8 40.4 + - + +
117F LYS* 3.9 10.4 - - + +
118F GLU 3.3 0.2 - - - -
119F LEU* 1.3 76.2 - - - +
121F ARG* 1.3 62.3 + - + +
123F ALA 4.8 4.3 - - - +
129F ILE* 4.4 11.0 - - + -
152F TYR* 5.2 0.2 + - - -
156F ASN* 3.3 33.5 + - - +
158F LEU* 4.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F ASN 4.6 2.8 + - - -
117F LYS* 3.0 43.5 + - + +
118F GLU* 3.5 31.0 + - - +
119F LEU 3.3 0.2 - - - -
120F GLN* 1.3 80.8 - - + +
122F GLN* 1.3 94.6 + - - +
123F ALA 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F TYR* 3.8 19.7 - - + +
118F GLU* 2.9 31.4 + - + +
121F ARG* 1.3 106.5 + - - +
123F ALA* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F TYR* 3.7 33.2 - - + +
92F ARG* 5.5 2.9 - - - +
118F GLU 4.0 0.2 + - - -
119F LEU* 3.1 32.7 + - + +
120F GLN 4.8 4.5 - - - +
121F ARG 5.0 0.3 - - - -
122F GLN* 1.3 85.3 + - - +
124F SER* 1.3 66.6 + - - +
125F PRO* 3.6 4.2 - - - +
127F ILE* 4.2 11.9 - - + -
----------------------------------------------------------
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