Contacts of the helix formed by residues 141 - 151 (chain B) in PDB entry 1KFV
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 ASP 141 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 3.9 24.8 + - - +
133B PRO* 5.2 0.6 - - - +
137B TYR 5.5 1.6 - - - -
138B GLU 5.0 2.4 + - - +
139B ASP 3.0 12.2 + - - +
140B PHE* 1.3 73.8 - - - +
142B GLU* 1.3 63.7 + - - +
143B LYS* 2.7 20.3 + - - +
144B LEU* 2.6 44.9 + - + +
145B PHE* 3.2 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B PHE 3.1 4.8 + - - -
141B ASP* 1.3 73.5 + - - +
143B LYS* 1.3 51.2 + - - +
145B PHE* 3.1 4.3 - - + +
146B ARG* 2.7 54.5 + - - +
197B ILE* 4.8 5.2 - - + -
198B HIS* 2.9 54.0 + - - +
201B HIS* 3.6 42.5 + - + +
202B ASP* 4.4 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 6.4 0.2 - - - +
141B ASP* 2.7 17.2 + - - +
142B GLU* 1.3 71.5 - - - +
144B LEU* 1.3 66.9 + - - +
146B ARG* 3.0 31.2 + - - +
147B GLU* 2.7 53.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PRO* 6.2 5.6 - - + -
141B ASP* 2.6 28.1 + - + +
143B LYS* 1.3 72.8 - - - +
145B PHE* 1.3 57.4 + - - +
147B GLU* 3.2 14.4 + - + +
148B LYS* 2.9 64.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B PHE* 3.5 31.6 - + + -
141B ASP 3.2 12.7 + - - +
142B GLU* 3.1 9.2 - - - +
143B LYS 3.0 0.2 - - - -
144B LEU* 1.3 79.9 - - - +
146B ARG* 1.3 61.2 - - - +
148B LYS* 3.4 5.5 + - + +
149B LEU* 3.0 56.8 + - + +
160B LEU* 4.3 7.9 - - + -
165B LEU* 3.7 33.4 - - + -
197B ILE* 3.8 15.7 - - + -
200B LEU* 3.7 23.8 - - + -
201B HIS* 3.8 31.0 - + + -
204B ILE* 3.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU* 2.7 44.9 + - - +
143B LYS* 3.5 36.2 + - - +
145B PHE* 1.3 72.6 - - - +
147B GLU* 1.3 66.9 + - + +
149B LEU* 3.2 3.3 + - - +
150B ARG* 3.1 40.7 + - - +
194B GLU* 3.5 32.0 + - - +
197B ILE* 4.0 29.9 - - + +
198B HIS* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LYS* 2.7 62.1 + - + +
144B LEU* 3.4 14.5 - - + +
146B ARG* 1.3 79.3 - - + +
148B LYS* 1.3 62.7 + - + +
149B LEU 3.3 0.2 + - - -
150B ARG* 3.3 10.1 + - - +
151B LYS* 3.3 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 2.9 46.5 + - + +
145B PHE* 3.8 6.1 - - - +
147B GLU* 1.3 75.9 - - + +
149B LEU* 1.3 62.2 + - - +
151B LYS* 3.4 25.8 + - - +
152B SER* 3.6 14.7 + - - -
159B TYR* 4.2 21.9 + - - +
164B THR* 4.0 21.5 + - - -
165B LEU* 4.8 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 3.0 54.7 + - + +
146B ARG 3.2 4.4 + - - +
148B LYS* 1.3 76.9 - - - +
150B ARG* 1.3 58.9 + - - +
151B LYS 3.6 0.2 + - - -
152B SER 3.7 0.2 - - - +
156B ILE* 3.9 13.2 - - + -
159B TYR* 4.7 0.7 - - + -
165B LEU* 3.5 26.9 - - + -
189B THR* 2.6 63.3 + - + +
190B ASN 3.1 0.9 + - - -
192B LEU* 4.6 2.2 - - + -
197B ILE* 3.9 28.3 - - + -
200B LEU* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ARG* 3.1 31.1 + - + +
147B GLU* 4.2 4.3 - - - +
149B LEU* 1.3 75.9 - - - +
151B LYS* 1.3 60.8 + - - +
152B SER 3.3 1.3 - - - -
189B THR 4.4 1.3 - - - +
190B ASN* 3.5 33.5 - - - +
192B LEU 4.6 11.4 + - - -
193B ILE* 5.7 0.8 - - - +
194B GLU* 2.5 45.4 + - - -
197B ILE* 5.6 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLU 3.3 15.7 + - - +
148B LYS* 3.7 16.7 - - - +
149B LEU 3.3 1.0 - - - -
150B ARG* 1.3 79.7 - - - +
152B SER* 1.3 57.3 + - - +
153B THR* 5.8 0.3 - - - +
----------------------------------------------------------
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