Contacts of the helix formed by residues 109 - 125 (chain B) in PDB entry 3KAV
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 GLU 109 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B CYS* 4.5 7.1 - - - -
56B THR 5.3 2.4 + - - -
57B GLU* 2.9 35.7 - - - +
108B ASP* 1.3 81.4 - - + +
110B PRO* 1.3 71.5 - - + +
111B LEU* 3.4 11.0 - - + +
112B GLU* 3.0 18.5 + - + +
113B ARG* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASP 3.8 2.0 - - - +
109B GLU* 1.3 88.3 - - + +
111B LEU* 1.3 58.4 + - + +
113B ARG* 3.1 12.7 - - + +
114B GLU* 2.7 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA 5.1 0.6 - - - +
50B ARG* 3.9 31.4 - - + +
51B TYR* 4.1 16.8 - - + +
54B LEU* 3.3 39.9 - - + +
55B CYS* 3.4 20.4 - - + +
109B GLU* 3.4 8.5 - - + +
110B PRO* 1.3 84.0 - - + +
112B GLU* 1.3 58.1 + - + +
114B GLU* 3.8 13.1 + - - +
115B CYS* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 4.3 15.1 - - + -
55B CYS* 4.1 7.6 - - - -
57B GLU* 2.7 38.2 - - - +
105B CYS 3.5 17.0 - - - +
106B ASP* 3.4 9.5 - - - +
107B GLY* 3.3 19.8 - - - +
108B ASP* 2.9 23.2 + - - +
109B GLU* 3.0 20.4 + - + +
111B LEU* 1.3 78.6 - - + +
113B ARG* 1.3 63.9 + - - +
115B CYS* 3.7 1.1 + - - +
116B ALA* 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASP* 3.5 13.6 + - - +
107B GLY 4.7 3.1 - - - +
108B ASP 5.0 7.0 - - - +
109B GLU 2.9 10.0 + - - +
110B PRO* 3.1 26.0 - - + +
112B GLU* 1.3 74.1 - - - +
114B GLU* 1.3 86.5 + - - +
116B ALA* 3.7 0.9 - - - +
117B GLY* 2.7 39.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 4.4 7.4 - - + +
50B ARG* 4.6 19.7 + - - +
110B PRO* 2.7 49.9 + - - +
111B LEU* 4.0 14.2 - - - +
113B ARG* 1.3 94.9 - - - +
115B CYS* 1.3 57.4 + - - +
117B GLY* 4.9 0.4 - - - -
118B ALA* 2.8 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 4.0 14.1 + - - +
48B CYS* 4.0 16.5 - - - -
51B TYR* 3.9 33.4 - - + -
101B CYS* 3.7 27.8 - - - -
105B CYS* 4.3 7.6 - - + -
111B LEU 3.1 18.6 + - - +
112B GLU* 4.0 2.7 - - - +
114B GLU* 1.3 77.9 - - - +
116B ALA* 1.3 63.3 + - - +
118B ALA* 4.0 1.9 - - - +
119B CYS* 3.1 27.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
101B CYS 5.5 0.2 - - - -
102B ALA* 3.8 24.0 - - + +
105B CYS 4.8 0.4 - - - -
106B ASP* 3.3 47.1 - - + +
112B GLU 3.2 7.1 + - - +
113B ARG 3.9 0.4 - - - +
115B CYS* 1.3 76.9 - - - +
117B GLY* 1.3 66.3 + - - +
119B CYS* 3.3 3.8 + - - +
120B ARG* 3.1 32.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
113B ARG* 2.7 29.7 + - - -
114B GLU* 3.6 1.1 - - - -
116B ALA* 1.3 71.7 - - - +
118B ALA* 1.3 55.9 + - - +
120B ARG* 2.8 32.9 + - - +
121B ARG* 2.8 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA 4.5 1.7 - - - +
43B ALA* 3.6 17.3 - - + +
44B CYS* 3.9 10.3 - - - +
47B ALA* 3.4 32.5 - - + -
114B GLU 2.8 11.2 + - - +
115B CYS 4.0 1.1 - - - +
117B GLY* 1.3 71.0 - - - +
119B CYS* 1.3 57.3 + - - +
121B ARG* 3.8 10.9 - - - +
122B PHE* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B CYS* 3.9 12.6 - - - -
48B CYS* 4.4 2.5 - - - -
69B CYS* 4.0 14.1 - - - -
98B ALA* 2.8 29.4 - - - +
99B LEU* 5.7 0.4 - - - -
101B CYS* 3.6 27.8 - - - -
102B ALA* 4.1 7.9 - - + -
115B CYS 3.1 22.6 + - - -
116B ALA 3.4 9.0 - - - +
117B GLY 3.1 1.0 - - - -
118B ALA* 1.3 76.1 - - - +
120B ARG* 1.3 62.5 + - - +
122B PHE* 3.4 2.8 + - - +
123B VAL* 3.1 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 6.3 1.4 - - - +
102B ALA* 4.2 28.2 + - + +
103B GLU* 5.7 2.6 - - - +
106B ASP* 4.1 19.0 + - - +
116B ALA* 3.1 18.0 + - - +
117B GLY* 2.8 13.4 + - - +
119B CYS* 1.3 74.6 - - - +
121B ARG* 1.3 60.7 + - - +
123B VAL* 3.1 8.2 + - - +
124B GLU* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG 5.9 0.4 + - - -
40B ALA* 4.2 19.7 - - + +
43B ALA* 5.4 8.7 - - - -
117B GLY 2.8 17.4 + - - +
118B ALA* 3.8 10.1 - - - +
120B ARG* 1.3 72.9 - - - +
122B PHE* 1.3 62.4 + - - +
124B GLU* 3.3 15.7 + - - +
125B ALA* 3.3 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B CYS* 4.1 13.0 - - - -
40B ALA* 3.7 15.5 - - - +
41B ALA* 3.5 39.3 - - + -
44B CYS* 4.2 5.4 - - + -
73B CYS* 3.9 11.9 - - - -
76B ALA* 5.0 3.4 - - + -
80B MSE 5.9 0.2 - - - -
91B CYS* 3.9 8.7 - - - -
94B ALA* 3.6 23.1 - - + -
95B ALA* 3.4 27.8 - - - -
98B ALA* 3.5 20.2 - - + -
118B ALA 2.9 18.8 + - - +
119B CYS 3.5 3.4 - - - +
120B ARG 3.1 0.2 - - - -
121B ARG* 1.3 73.6 - - - +
123B VAL* 1.3 60.8 + - - +
125B ALA* 2.9 21.7 + - - +
126B CYS* 3.3 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA* 3.7 23.1 - - + +
98B ALA* 3.6 22.4 - - + -
99B LEU* 4.3 19.5 - - + +
119B CYS 3.1 16.8 - - - +
120B ARG* 3.1 8.2 + - - +
122B PHE* 1.3 75.5 - - - +
124B GLU* 1.3 58.5 + - + +
126B CYS* 2.9 30.4 + - + +
127B ARG* 3.5 15.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 3.3 11.7 + - - -
120B ARG* 2.8 44.4 + - + +
121B ARG* 3.3 13.8 + - - +
123B VAL* 1.3 76.6 - - + +
125B ALA* 1.3 55.5 + - - +
126B CYS 3.3 0.7 - - - -
127B ARG* 4.3 8.9 + - - +
128B PRO* 3.5 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PRO 4.2 2.6 - - - +
36B ARG* 3.1 25.5 + - - +
37B CYS* 3.2 41.3 - - - +
40B ALA* 3.9 9.2 - - + -
121B ARG* 3.3 10.8 + - + +
122B PHE 2.9 11.1 + - - +
124B GLU* 1.3 76.0 - - - +
126B CYS* 1.3 59.7 + - - +
128B PRO* 3.5 12.4 - - - +
----------------------------------------------------------
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