Contacts of the helix formed by residues 138 - 149 (chain A) in PDB entry 1KI1
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 138 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 4.1 3.6 - - - +
136A PRO 3.6 3.6 + - - -
137A ILE* 1.3 78.0 - - - +
139A PRO* 1.3 71.9 - - - +
140A GLU* 2.7 32.1 + - + +
141A THR* 2.8 53.1 + - - +
142A ALA* 3.0 10.3 + - - +
154A TYR* 5.4 0.2 - - - -
156A GLU* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 3.5 21.9 - - - +
138A THR* 1.3 89.5 - - - +
140A GLU* 1.3 72.0 + - - +
142A ALA* 3.6 0.9 - - + +
143A GLU* 2.8 43.1 + - - +
154A TYR* 3.9 19.7 - - + -
156A GLU* 3.9 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 2.7 34.1 + - + +
139A PRO* 1.3 90.6 - - - +
141A THR* 1.3 62.4 + - - +
143A GLU* 3.2 19.0 + - - +
144A LYS* 3.0 23.2 + - - +
147A ARG* 5.0 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.7 26.7 - - + -
137A ILE* 4.2 11.4 - - + -
138A THR* 2.8 29.9 + - - +
140A GLU* 1.3 76.3 - - - +
142A ALA* 1.3 61.1 + - - +
144A LYS* 3.5 9.8 + - + +
145A LEU* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 3.9 15.5 - - + -
90A PHE* 4.0 11.2 - - + -
112A LEU* 3.5 6.3 - - + +
137A ILE* 4.4 0.7 - - + -
138A THR 3.0 10.8 + - - +
139A PRO 3.6 2.2 - - - +
141A THR* 1.3 77.3 - - - +
143A GLU* 1.3 59.7 + - - +
145A LEU 3.2 1.9 + - - -
146A ALA* 2.8 29.1 + - - +
154A TYR* 3.4 44.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PRO* 2.8 34.6 + - - +
140A GLU* 3.2 24.0 + - - +
142A ALA* 1.3 71.5 - - - +
144A LYS* 1.3 63.3 + - - +
146A ALA* 3.3 9.3 + - - +
147A ARG* 3.1 39.6 + - + +
154A TYR* 4.1 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU 3.0 13.9 + - - +
141A THR* 3.6 13.2 - - + +
142A ALA 3.1 0.2 - - - -
143A GLU* 1.3 77.2 - - - +
145A LEU* 1.3 63.2 + - - +
147A ARG* 3.0 40.5 + - - +
148A ASP* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.6 43.7 - - + +
93A VAL* 4.0 19.1 - - + -
94A LYS* 4.0 32.8 - - + +
112A LEU* 4.3 5.8 - - + -
141A THR 3.2 2.4 + - - +
142A ALA 3.2 8.3 + - - +
144A LYS* 1.3 80.3 - - - +
146A ALA* 1.3 62.1 + - - +
148A ASP* 4.3 11.9 - - + +
149A LEU* 3.0 52.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.8 15.7 - - + +
142A ALA 2.8 13.4 + - - +
143A GLU* 3.4 14.1 - - - +
144A LYS 3.1 0.2 - - - -
145A LEU* 1.3 78.2 - - - +
147A ARG* 1.3 62.0 + - + +
149A LEU* 5.1 0.7 - - - -
150A LYS 3.0 3.5 + - - -
151A ALA* 2.9 46.1 + - + +
153A LYS* 4.3 3.6 - - - -
154A TYR* 4.1 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU 5.0 1.6 + - - -
143A GLU* 3.1 21.0 + - - +
144A LYS* 3.0 57.0 + - - +
146A ALA* 1.3 75.7 - - + +
148A ASP* 1.3 68.8 + - - +
150A LYS* 3.1 20.1 + - - +
151A ALA 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 3.0 28.9 + - - +
145A LEU* 3.8 15.4 - - + +
146A ALA 3.4 0.2 - - - -
147A ARG* 1.3 82.2 + - - +
149A LEU* 1.3 65.5 + - + +
150A LYS* 3.5 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 3.9 5.2 - - + -
94A LYS* 3.8 29.8 - - + +
98A VAL* 3.7 36.1 - - + +
99A PRO* 6.0 0.4 - - + -
110A PHE* 3.5 23.5 - - + -
112A LEU* 5.6 2.0 - - + -
145A LEU* 3.0 47.1 + - + +
146A ALA* 4.4 1.6 - - - +
148A ASP* 1.3 77.8 - - + +
150A LYS* 1.3 72.2 + - - +
----------------------------------------------------------
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