Contacts of the helix formed by residues 146 - 157 (chain B) in PDB entry 4K71
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 LYS 146 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASP* 6.1 0.7 - - - +
93A LYS* 5.9 5.4 - - - +
104A GLN* 5.2 7.7 + - - -
144B GLN 3.2 2.0 + - - -
145B ASP* 1.3 82.6 - - + +
147B ALA* 1.3 57.7 + - - +
148B ALA 3.4 2.2 - - - -
149B ASN* 3.3 21.4 + - + +
150B LYS* 2.8 62.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 6.2 1.6 - - - -
74B LEU* 4.2 23.1 - - + +
127B TRP* 3.7 11.8 - - + -
141B TRP 3.5 23.8 - - - +
144B GLN* 3.4 15.7 + - + +
145B ASP 3.3 5.0 + - - +
146B LYS* 1.3 76.6 - - - +
148B ALA* 1.3 58.6 + - - +
150B LYS* 3.3 7.8 + - - +
151B GLU* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 3.9 2.7 - - + -
125B GLY 3.5 24.7 - - - +
127B TRP* 3.6 16.0 - - + -
141B TRP 4.9 0.2 + - - -
142B GLN* 3.6 21.3 + - - +
144B GLN 4.9 0.8 + - - -
146B LYS 3.4 0.2 - - - -
147B ALA* 1.3 77.5 - - - +
149B ASN* 1.3 65.0 + - - +
151B GLU* 3.3 4.3 + - - +
152B LEU* 3.0 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.2 17.3 + - - +
86A GLU* 3.8 2.2 - - - -
89A ASP* 3.5 39.2 + - - +
92A ALA* 6.2 1.8 - - - +
93A LYS* 6.2 1.4 - - - +
146B LYS* 3.3 21.8 + - + +
148B ALA* 1.3 80.2 - - - +
150B LYS* 1.3 61.8 + - + +
152B LEU* 3.3 9.9 + - - +
153B THR* 3.1 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 3.8 24.9 - - - +
70B ILE* 4.3 42.4 - - + +
71B LYS* 5.2 2.0 - - - +
145B ASP 4.8 2.8 + - - -
146B LYS* 2.8 56.6 + - + +
147B ALA* 3.8 5.8 - - - +
149B ASN* 1.3 72.5 - - + +
151B GLU* 1.3 59.0 + - - +
153B THR* 3.6 3.1 + - - +
154B PHE* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 2.7 33.4 + - - +
74B LEU* 5.8 2.7 - - + +
94B LEU* 3.9 11.0 - - - +
108B ALA* 5.4 0.6 - - - +
110B PHE* 3.9 14.4 - - - -
120B PHE* 3.7 30.0 - - + +
127B TRP* 3.3 32.4 + - + -
141B TRP* 5.4 0.5 - - - -
147B ALA 3.0 17.0 + - - +
148B ALA 3.6 5.2 - - - +
149B ASN 3.2 0.2 - - - -
150B LYS* 1.3 74.3 - - - +
152B LEU* 1.3 66.0 + - - +
154B PHE* 3.1 3.7 + - - +
155B LEU* 2.9 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.5 31.6 - - - +
120B PHE* 4.1 11.7 - - + -
122B LEU* 3.6 33.4 - - + +
125B GLY* 4.3 14.4 - - - +
148B ALA* 3.0 18.9 + - + +
149B ASN* 3.5 13.7 - - - +
151B GLU* 1.3 76.6 - - - +
153B THR* 1.3 53.0 + - - +
155B LEU* 3.7 2.0 - - - -
156B LEU* 2.8 59.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.1 22.6 + - - +
85A GLY 4.0 0.2 - - - -
86A GLU* 2.8 54.1 + - + +
149B ASN 3.1 4.4 + - - -
150B LYS 3.7 3.8 - - - +
152B LEU* 1.3 76.2 - - - +
154B PHE* 1.3 63.2 + - - +
157B PHE* 2.9 23.9 + - + -
158B SER* 2.8 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 3.5 46.4 - + - -
11B LEU* 6.2 0.2 - - + -
64B GLU* 5.4 0.4 - - - -
67B ASP* 3.9 26.2 - - + -
68B LEU* 4.7 6.7 - - + -
71B LYS* 3.6 37.7 - - + +
94B LEU* 4.3 14.1 - - + -
150B LYS 2.9 19.9 + - - +
151B GLU* 3.1 5.1 + - - +
153B THR* 1.3 75.6 - - - +
155B LEU* 1.3 72.7 + - + +
158B SER* 3.7 8.1 - - - -
159B CYS* 2.9 35.7 + - + +
162B ARG* 3.6 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 4.2 7.9 - - + -
95B GLY* 4.0 19.5 - - - +
96B CYS* 4.4 7.4 - - - +
104B SER* 5.7 0.7 - - - -
106B PRO* 4.4 10.9 - - + +
107B THR 4.0 17.0 - - - +
108B ALA* 3.8 23.8 - - + -
120B PHE* 3.9 21.1 - - + -
122B LEU* 3.9 18.4 - - + -
151B GLU* 2.9 29.3 + - + +
152B LEU 3.9 2.0 - - - +
154B PHE* 1.3 93.7 - - + +
156B LEU* 1.3 60.3 + - - +
157B PHE 3.6 0.2 - - - -
159B CYS* 3.8 5.3 - - + +
160B PRO* 3.3 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 4.4 15.9 - - + -
82A GLU* 3.5 52.7 - - + +
104B SER* 5.5 5.1 - - - +
106B PRO* 3.9 26.9 - - + -
122B LEU* 4.0 16.8 - - + +
152B LEU* 2.8 46.7 + - + +
155B LEU* 1.3 74.1 - - - +
157B PHE* 1.3 57.0 + - - +
160B PRO* 3.6 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 5.5 9.0 - - + -
81A ARG 3.5 19.7 - - - +
82A GLU 3.4 17.7 - - - -
83A THR 3.4 20.9 - - - -
84A TYR 4.4 1.1 - - - -
85A GLY* 3.6 22.2 - - - -
153B THR* 2.9 18.6 + - + +
156B LEU* 1.3 78.3 - - - +
158B SER* 1.3 80.7 + - - +
159B CYS 3.4 1.7 + - - -
160B PRO* 3.4 1.6 - - - +
161B HIS* 3.0 55.7 + + + +
----------------------------------------------------------
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