Contacts of the helix formed by residues 104 - 122 (chain B) in PDB entry 4YYJ
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 THR 104 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 6.1 1.3 - - + -
100B ASN* 3.5 9.9 - - + +
101B ARG* 2.7 35.6 + - + +
102B PRO 3.3 0.4 - - - -
103B ASP* 1.3 90.7 - - - +
105B VAL* 1.3 66.4 + - - +
106B TYR* 3.2 16.3 + - + -
107B TYR* 3.2 15.9 + - - +
108B LYS* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B HIS* 5.8 1.6 - - + -
44B PHE* 3.5 33.4 - - + -
103B ASP 3.9 0.8 + - - -
104B THR* 1.3 73.5 - - - +
106B TYR* 1.3 65.2 + - + +
108B LYS* 3.9 6.1 - - - +
109B LEU* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 3.7 46.2 - + + -
96B ALA* 4.6 0.4 - - - +
100B ASN* 3.5 37.5 - - - +
104B THR* 3.1 14.2 - - + +
105B VAL* 1.3 83.8 - - + +
107B TYR* 1.3 57.7 + - - +
109B LEU* 3.8 4.0 - - - +
110B ALA* 3.0 30.7 + - - +
4C GLY* 3.6 30.2 + - - -
5C BTK 3.7 54.6 - - + +
6C GLY 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA 4.6 4.0 - - - -
97B MET* 3.4 42.7 - - + +
100B ASN* 3.5 23.3 - - + +
101B ARG 3.2 19.5 - - - +
102B PRO* 3.5 44.5 - - + +
104B THR* 3.2 3.8 + - - +
106B TYR* 1.3 75.0 - - - +
108B LYS* 1.3 71.9 + - + +
110B ALA* 3.3 4.7 + - - +
111B LYS* 3.0 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PRO 3.9 11.0 - - - +
103B ASP* 3.6 29.9 + - - +
104B THR 3.1 13.3 + - - +
105B VAL* 3.9 5.2 - - - +
107B TYR* 1.3 83.3 - - + +
109B LEU* 1.3 63.0 + - - +
111B LYS* 3.6 4.7 + - - +
112B LYS* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS 3.8 10.3 - - - +
40B ASP* 3.7 31.9 - - + +
41B PRO* 5.6 2.7 - - + -
44B PHE* 4.2 15.7 - - + -
45B PHE* 3.7 19.7 - - + -
105B VAL* 2.9 20.7 + - + +
106B TYR* 3.8 4.9 - - - +
108B LYS* 1.3 75.0 - - - +
110B ALA* 1.3 60.0 + - - +
112B LYS* 3.1 17.1 + - + +
113B ILE* 2.8 48.9 + - + +
5C BTK 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 3.7 14.3 - - + -
93B CYS* 3.8 15.5 - - - +
96B ALA* 3.6 26.9 - - + -
97B MET* 3.8 7.6 - - + -
106B TYR 3.0 18.7 + - - +
107B TYR 3.3 3.8 + - - +
109B LEU* 1.3 76.9 - - - +
111B LYS* 1.3 57.7 + - - +
113B ILE* 3.7 4.7 - - - +
114B LEU* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 3.7 20.5 - - - -
107B TYR* 3.0 37.0 + - + +
108B LYS* 4.0 4.9 - - - +
110B ALA* 1.3 75.4 - - - +
112B LYS* 1.3 63.7 + - - +
114B LEU* 4.5 1.8 - - - -
115B HIS* 3.3 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS* 5.6 4.9 - - - -
108B LYS 3.1 19.5 + - - +
109B LEU* 3.1 20.4 + - + +
111B LYS* 1.3 77.1 - - - +
113B ILE* 1.3 63.8 + - + +
115B HIS* 4.2 1.4 - - - +
116B ALA* 3.1 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 5.2 2.7 - - + +
39B LYS* 3.9 31.6 - - + +
40B ASP* 5.1 2.5 - - + -
45B PHE* 3.7 32.5 - - + -
67B PHE* 4.5 7.9 - - + -
89B PHE* 3.4 24.8 - - + -
92B MET* 4.4 3.6 - - + -
93B CYS* 3.8 10.3 - - - -
109B LEU* 2.8 41.4 + - + +
110B ALA* 3.7 4.7 - - - +
112B LYS* 1.3 80.0 - - + +
114B LEU* 1.3 62.7 + - - +
116B ALA* 4.4 5.4 - - - +
117B GLY* 2.7 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.9 2.4 - - + -
90B LYS* 4.0 18.2 - - + -
93B CYS* 3.7 23.8 - - + -
94B ASP* 4.0 9.9 - - - +
97B MET* 3.7 26.9 - - + -
110B ALA 2.8 20.8 + - - +
111B LYS 3.8 3.8 - - - +
113B ILE* 1.3 77.4 - - - +
115B HIS* 1.3 78.9 + - + +
118B PHE* 3.0 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 6.2 0.9 - - + -
111B LYS* 3.3 43.0 + - + +
112B LYS* 4.4 1.3 - - - +
114B LEU* 1.3 99.7 - - + +
116B ALA* 1.3 62.5 + - - +
118B PHE* 4.0 4.0 - - + +
119B LYS* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS* 4.1 23.0 + - + +
112B LYS* 3.1 24.7 + - + +
113B ILE* 4.1 3.6 - - - +
115B HIS* 1.3 73.9 - - - +
117B GLY* 1.3 59.8 + - - +
119B LYS* 3.3 8.8 + - - +
120B MET* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.5 24.9 - - - -
39B LYS* 4.7 2.7 - - - +
89B PHE* 3.9 2.7 - - - -
113B ILE 2.7 21.7 + - - -
116B ALA* 1.3 73.7 - - - +
118B PHE* 1.3 63.1 + - - +
120B MET* 3.2 4.5 + - - +
121B MET* 3.1 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LYS* 3.5 55.6 + - + -
87B ALA* 5.4 0.2 - - - -
89B PHE* 3.8 24.7 - + - -
90B LYS* 3.9 17.9 - - + -
114B LEU* 3.0 40.0 + - + +
115B HIS* 4.0 4.9 - - + +
117B GLY* 1.3 77.1 - - - +
119B LYS* 1.3 62.0 - - - +
121B MET* 3.4 7.3 + - + +
122B SER* 3.2 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B HIS 3.1 17.5 + - - +
116B ALA* 3.6 8.7 - - - +
118B PHE* 1.3 78.3 - - - +
120B MET* 1.3 60.4 + - - +
122B SER* 3.3 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 4.0 23.2 - - - +
35B GLN* 3.4 53.2 - - + +
36B LEU* 3.4 35.9 - - + +
39B LYS* 4.5 12.8 - - - +
116B ALA 2.9 16.7 + - - +
117B GLY 3.6 0.7 - - - +
119B LYS* 1.3 77.1 - - - +
121B MET* 1.3 69.1 + - + +
122B SER 3.1 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.7 43.3 - - + -
36B LEU* 4.1 10.5 - - + -
82B VAL* 5.0 2.8 - - - +
85B PHE* 3.5 31.9 - - + -
86B LYS* 3.5 43.7 + - + -
89B PHE* 3.8 29.2 - - + -
117B GLY 3.1 22.0 + - - +
118B PHE* 3.8 4.7 - - + +
120B MET* 1.3 85.0 - - + +
122B SER* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LYS* 3.8 15.1 + - - -
118B PHE 3.2 14.1 + - - -
119B LYS* 3.7 15.5 - - - -
120B MET 3.1 5.6 - - - +
121B MET* 1.3 79.9 - - - +
----------------------------------------------------------
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