Contacts of the helix formed by residues 125 - 136 (chain B) in PDB entry 3KJR
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 GLY 125 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B THR* 3.1 7.1 + - - -
124B GLY* 1.3 71.7 - - - -
126B SER* 1.3 56.4 + - - -
127B PHE 3.1 2.0 - - - -
128B LEU 3.0 2.6 + - - -
129B TYR* 2.8 40.5 + - - -
512B NAP 2.6 44.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.3 5.2 - - - +
125B GLY* 1.3 71.0 - - - -
127B PHE* 1.3 61.2 + - - +
129B TYR* 3.8 11.7 - - - +
130B LYS* 2.9 34.3 + - - +
154B THR* 3.1 19.2 - - - +
155B TYR 2.3 33.4 + - - -
157B PRO* 4.4 4.4 - - - +
512B NAP 2.9 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY 3.1 0.6 - - - -
126B SER* 1.3 81.1 - - - +
128B LEU* 1.3 61.2 + - - +
130B LYS* 3.4 5.3 - - - +
131B GLU* 3.3 17.7 + - - +
512B NAP 3.3 82.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.6 29.4 - - + +
65B PHE 3.7 20.6 - - - +
66B GLY* 4.6 0.4 - - - +
88B LEU* 3.7 23.8 - - + -
104B LEU* 3.8 25.8 - - + -
122B ILE* 3.7 20.0 - - + -
124B GLY 3.7 11.9 - - - +
125B GLY 3.0 9.0 + - - +
127B PHE* 1.3 77.1 - - - +
129B TYR* 1.3 64.0 + - - +
131B GLU* 3.6 1.0 + - - +
132B VAL* 3.1 31.5 + - + +
512B NAP 3.4 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 3.6 37.0 - - + -
14B PHE 2.8 19.9 + - - -
15B VAL* 3.5 26.3 - - + +
23B ILE* 3.8 15.7 - - + -
122B ILE* 3.7 17.5 - - + -
123B LEU 3.4 3.8 + - - -
124B GLY* 3.3 30.5 - - - -
125B GLY 2.8 27.2 + - - +
126B SER* 3.8 7.0 - - - +
128B LEU* 1.3 72.1 - - - +
130B LYS* 1.3 56.2 + - - +
132B VAL* 3.4 5.8 + - - +
133B LEU* 3.0 35.1 + - + +
156B PHE* 3.6 18.6 - + + -
157B PRO* 3.9 16.6 - - + -
512B NAP 3.6 5.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER* 2.9 18.2 + - - +
127B PHE* 3.4 8.7 - - - +
129B TYR* 1.3 77.1 - - - +
131B GLU* 1.3 57.9 + - - +
133B LEU* 4.1 0.8 - - - +
134B ASP* 2.8 59.3 + - - +
157B PRO* 3.8 31.4 - - + +
158B ASP 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 2.6 38.0 + - + +
103B ASP* 5.3 2.9 - - - +
104B LEU* 3.7 28.5 + - + +
105B SER* 4.6 3.3 + - - -
127B PHE 3.3 3.9 + - - +
128B LEU 4.1 2.7 - - - +
129B TYR 3.5 0.2 - - - -
130B LYS* 1.3 78.1 - - - +
132B VAL* 1.3 63.4 + - - +
134B ASP* 4.6 2.7 - - - -
135B ASN* 2.8 36.6 + - - +
137B LEU* 4.5 0.7 - - + +
512B NAP 2.4 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.1 17.7 - - + -
13B ILE* 4.0 15.0 - - + -
104B LEU* 3.7 22.2 - - + -
122B ILE* 4.2 16.8 - - + -
128B LEU* 3.1 19.7 + - + +
129B TYR* 3.6 4.5 - - - +
131B GLU* 1.3 75.4 - - - +
133B LEU* 1.3 60.4 + - - +
136B GLY 3.4 2.4 + - - -
137B LEU* 2.9 41.8 + - + +
138B CYS* 3.5 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 4.2 7.6 - - + -
129B TYR 3.0 20.3 + - - +
130B LYS* 4.1 2.0 - - - +
132B VAL* 1.3 73.4 - - - +
134B ASP* 1.3 66.3 + - - +
135B ASN 3.0 4.0 + - - -
136B GLY* 3.2 12.3 + - - +
138B CYS* 4.3 11.0 - - + -
141B ILE* 4.2 12.6 - - + -
156B PHE* 4.1 27.8 - - + -
157B PRO* 4.4 15.5 - - + -
158B ASP 4.3 17.3 - - - +
159B ILE* 5.2 0.2 - - + -
160B PRO* 4.1 24.1 - - + +
163B PHE* 4.0 33.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LYS* 2.8 53.6 + - - +
131B GLU* 4.1 4.7 - - - +
133B LEU* 1.3 74.6 - - - +
135B ASN* 1.3 66.3 + - - +
157B PRO* 6.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 3.2 46.9 + - + -
131B GLU* 2.8 31.4 + - - +
133B LEU 3.1 0.6 - - - -
134B ASP* 1.3 83.8 - - - +
136B GLY* 1.3 61.2 + - - +
137B LEU* 4.1 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 5.3 1.7 - - - -
132B VAL 3.4 1.0 + - - -
133B LEU* 3.2 13.7 + - - -
135B ASN* 1.3 79.6 - - - +
137B LEU* 1.3 62.1 + - - +
138B CYS 3.3 8.4 + - - +
139B ASP* 4.6 4.2 - - - +
186B ARG* 4.4 25.1 + - - -
----------------------------------------------------------
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