Contacts of the helix formed by residues 91 - 106 (chain B) in PDB entry 1YKI
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 ASP 91 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 2.7 32.9 + - - -
89B ALA* 3.4 5.4 + - + +
90B MET* 1.3 80.5 - - - +
92B ASP* 1.3 63.8 + - - +
93B VAL* 3.4 15.3 + - + +
94B TRP* 3.1 35.5 + - - +
95B LEU* 3.3 10.4 + - - +
129B ARG* 3.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP* 1.3 71.0 - - - +
93B VAL* 1.3 66.8 + - + +
94B TRP 3.2 0.2 - - - -
95B LEU* 3.3 9.7 + - - +
96B LYS* 3.0 23.7 + - - +
122B LYS* 4.7 9.9 - - - -
129B ARG* 2.8 33.8 + - - +
130B LYS* 5.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP* 3.3 11.9 + - + +
92B ASP* 1.3 78.2 - - + +
94B TRP* 1.3 58.9 + - + +
96B LYS* 3.3 8.8 + - + +
97B LEU* 2.9 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 3.4 23.3 - - + -
212A ILE* 3.9 17.3 - - + -
213A THR* 4.7 1.8 - - + -
43B SER 2.8 26.9 + - - -
44B GLN 3.3 19.3 + - - -
46B TRP 4.3 10.8 - - - -
87B LYS* 3.6 30.2 - - + +
90B MET* 3.8 18.2 - - + -
91B ASP* 3.1 26.7 + - - +
92B ASP 3.2 0.4 - - - -
93B VAL* 1.3 76.7 - - + +
95B LEU* 1.3 66.3 + - + +
97B LEU* 3.1 20.8 + - + +
98B VAL* 3.0 34.3 + - + +
183B TYR* 3.5 26.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B SER* 5.3 3.1 - - - -
90B MET* 3.5 32.5 - - + -
91B ASP 3.3 8.0 + - - +
92B ASP* 3.3 12.2 + - - +
94B TRP* 1.3 80.1 - - + +
96B LYS* 1.3 62.3 + - - +
98B VAL* 3.5 5.1 + - + +
99B VAL* 3.2 24.0 + - - +
118B ASP* 4.7 3.5 - - - +
121B ARG* 3.8 35.3 + - + -
122B LYS* 4.2 22.2 - - + -
125B ALA* 4.2 13.5 - - + -
129B ARG* 3.6 39.3 - - - +
138B TRP* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASP 3.0 17.2 + - - +
93B VAL* 3.6 7.4 - - + +
95B LEU* 1.3 75.2 - - - +
97B LEU* 1.3 58.3 + - - +
99B VAL* 3.3 8.9 + - + +
100B ASP* 2.8 67.7 + - - +
118B ASP* 5.4 1.8 - - - -
122B LYS* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 3.5 34.8 - - + -
212A ILE* 3.9 27.6 - - + -
93B VAL* 2.9 19.4 + - + +
94B TRP* 3.3 31.4 - - + +
96B LYS* 1.3 77.1 - - - +
98B VAL* 1.3 56.8 + - - +
100B ASP* 3.9 5.7 - - + +
101B GLN* 3.0 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 4.3 20.0 - - + -
42B ASN* 3.2 25.1 - - + +
43B SER* 3.8 23.8 - - - +
44B GLN* 4.3 6.5 - - - +
94B TRP* 3.0 27.6 + - + +
95B LEU* 3.8 6.5 - - + +
96B LYS 3.2 0.2 - - - -
97B LEU* 1.3 77.9 - - + +
99B VAL* 1.3 58.3 + - - +
101B GLN* 3.3 2.5 + - - +
102B GLU* 3.0 30.4 + - - +
121B ARG* 3.7 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU 3.2 9.8 + - - +
96B LYS* 3.3 16.8 - - + +
98B VAL* 1.3 79.5 - - - +
100B ASP* 1.3 69.0 + - - +
102B GLU* 3.4 4.1 + - - -
103B ASP* 3.0 27.0 + - - +
108B PHE* 3.6 15.8 - - + -
114B LYS* 3.9 23.6 - - + +
117B ASN* 3.6 23.6 - - - +
118B ASP* 4.1 19.3 - - + +
121B ARG* 3.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LYS* 2.8 55.2 + - - +
97B LEU* 3.9 5.7 - - + +
99B VAL* 1.3 78.8 - - - +
101B GLN* 1.3 57.5 + - - +
103B ASP* 3.3 3.5 + - - +
104B ALA* 2.9 27.7 + - - +
114B LYS* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 3.5 7.9 - - - +
207A ARG 3.4 29.3 + - - +
208A LEU* 4.0 12.0 - - + +
209A PRO* 3.6 19.8 - - - +
44B GLN* 5.9 1.3 - - - +
97B LEU 3.0 18.6 + - - +
98B VAL 3.7 4.7 - - - +
100B ASP* 1.3 75.4 - - - +
102B GLU* 1.3 64.6 + - - +
104B ALA* 3.2 11.7 + - - +
105B ASP* 2.9 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 3.2 22.7 - - - +
1218A FMN 4.6 3.3 + - - -
42B ASN* 2.9 33.8 + - - +
98B VAL* 3.0 16.7 + - - +
99B VAL* 3.4 7.8 + - - +
101B GLN* 1.3 75.0 - - - +
103B ASP* 1.3 60.0 + - - +
105B ASP* 3.4 1.6 + - - +
106B GLY 3.2 4.7 + - - -
107B ARG* 3.1 48.8 + - - +
108B PHE* 3.6 14.5 - - + -
117B ASN* 3.1 20.0 + - - +
121B ARG* 3.0 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL 3.0 13.7 + - - +
100B ASP 3.4 9.4 - - - +
102B GLU* 1.3 73.9 - - - +
104B ALA* 1.3 63.6 + - - +
106B GLY* 3.1 13.9 + - - -
107B ARG 4.9 0.7 - - - +
108B PHE* 3.6 27.4 + - + +
114B LYS* 2.9 36.5 + - - +
1225B DMS 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ASP 2.9 14.5 + - - +
101B GLN* 3.2 19.9 + - - +
103B ASP* 1.3 76.7 - - - +
105B ASP* 1.3 61.0 + - - +
106B GLY 3.4 0.5 + - - -
1225B DMS 3.6 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PRO* 3.1 21.9 - - + +
205A LYS 4.0 9.4 - - - +
206A SER* 2.8 39.7 + - - -
207A ARG 3.8 3.1 + - - +
101B GLN* 2.9 34.6 + - - +
102B GLU 3.8 5.2 - - - +
104B ALA* 1.3 78.5 - - - +
106B GLY* 1.3 57.5 + - - +
107B ARG* 3.7 0.4 - - + -
1225B DMS 3.5 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 4.4 4.5 - - - +
204A PRO* 3.7 15.0 - - - +
102B GLU 3.2 0.2 + - - -
103B ASP 3.1 13.8 + - - -
104B ALA 3.3 0.6 - - - -
105B ASP* 1.3 79.4 - - - +
107B ARG* 1.3 62.9 + - - +
108B PHE 3.3 9.6 + - - +
1225B DMS 4.1 15.9 - - - -
----------------------------------------------------------
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