Contacts of the helix formed by residues 215 - 227 (chain A) in PDB entry 4KN1
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 PRO 215 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLY* 6.3 0.4 - - - -
201A GLY* 5.3 0.7 - - - -
205A GLN* 4.0 21.1 - - - +
208A PHE* 3.6 40.2 - - + -
209A ASP 4.6 2.0 - - - +
213A GLY 3.4 10.0 - - - +
214A ASN* 1.3 88.5 - - - +
216A ASN* 1.3 66.1 + - - +
217A GLU 3.3 1.3 + - - -
218A GLU* 3.8 18.6 + - + +
219A VAL* 3.7 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.6 1.4 - - - +
106A ASN* 3.6 8.7 - - + +
107A LEU* 6.4 0.2 - - + -
203A CYS 3.8 4.7 - - - +
204A ILE* 3.4 28.5 - - + +
205A GLN* 2.9 49.1 + - - +
208A PHE* 3.9 10.9 - - - -
214A ASN* 2.8 8.5 + - - +
215A PRO* 1.3 82.5 - - - +
217A GLU* 1.3 59.7 + - - +
218A GLU 3.4 0.2 - - - -
219A VAL* 3.6 6.4 - - - +
220A ALA* 2.9 28.4 + - - +
302A K 3.5 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 5.3 0.2 - - - +
57A ASN* 5.4 13.1 + - - +
106A ASN* 3.6 30.2 - - - +
214A ASN* 3.5 32.0 + - + +
215A PRO 3.3 0.6 - - - -
216A ASN* 1.3 74.3 - - - +
218A GLU* 1.3 67.1 + - - +
220A ALA* 3.1 4.5 + - - +
221A ARG* 2.9 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A SER 5.3 0.7 - - - +
201A GLY* 3.7 29.0 - - - +
202A ARG* 4.3 11.7 + - - +
214A ASN 4.6 0.6 + - - +
215A PRO* 3.8 12.4 + - + +
217A GLU* 1.3 78.7 - - - +
219A VAL* 1.3 57.6 + - - +
221A ARG* 3.4 23.9 + - - +
222A PHE* 2.9 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TRP* 4.3 1.8 - - + -
127A PRO* 5.0 0.2 - - + -
201A GLY* 3.4 30.5 - - - +
203A CYS 3.5 28.0 - - - +
204A ILE* 3.4 25.1 - - + +
215A PRO* 3.7 15.3 - - + +
216A ASN* 3.6 10.1 - - - +
217A GLU 3.1 1.0 - - - -
218A GLU* 1.3 75.2 - - - +
220A ALA* 1.3 64.3 + - - +
222A PHE* 3.2 2.2 + - - +
223A TYR* 3.1 48.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU 5.7 0.2 - - - +
28A LEU* 3.6 14.9 - - + +
106A ASN* 3.4 37.7 - - + +
109A PRO* 3.6 14.2 - - + +
110A TRP* 4.3 4.9 - - - -
204A ILE* 4.8 0.2 - - - +
216A ASN 2.9 10.5 + - - +
217A GLU 3.5 7.9 - - - +
219A VAL* 1.3 76.6 - - - +
221A ARG* 1.3 58.1 + - - +
223A TYR 3.5 0.2 + - - -
224A ALA* 3.0 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 5.8 0.3 - - - +
28A LEU* 3.6 29.4 - - + +
217A GLU* 2.9 27.3 + - - +
218A GLU* 3.6 33.1 - - - +
220A ALA* 1.3 79.0 - - - +
222A PHE* 1.3 63.1 + - - +
224A ALA* 3.7 2.8 + - - +
225A ALA* 3.6 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TYR* 6.2 0.2 - + - -
201A GLY 4.7 0.2 - - - +
202A ARG* 3.4 60.1 - - - +
218A GLU* 2.9 18.5 + - + +
219A VAL* 3.2 5.8 + - - +
221A ARG* 1.3 78.0 - - - +
223A TYR* 1.3 86.5 + + - +
225A ALA* 3.3 6.7 + - - +
226A ALA* 2.9 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 4.7 0.9 - - + -
110A TRP* 3.6 28.7 - + + -
127A PRO* 4.2 15.4 - - + +
192A LYS* 5.8 5.2 - - - -
194A SER* 4.9 0.5 + - - -
196A TYR* 3.8 18.6 - + - -
202A ARG* 2.5 39.9 + - - +
219A VAL* 3.1 36.1 + - + +
222A PHE* 1.3 97.3 - + - +
224A ALA* 1.3 61.1 + - - +
225A ALA 3.0 2.2 - - - -
226A ALA* 4.0 6.5 - - + +
227A MET* 2.7 55.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 3.8 37.5 - - + +
27A LEU* 4.6 10.0 - - + +
28A LEU* 3.8 12.8 - - + -
109A PRO* 4.1 16.0 - - + +
220A ALA 3.0 20.2 + - - +
221A ARG 3.7 6.3 - - - +
223A TYR* 1.3 76.9 - - - +
225A ALA* 1.3 59.0 + - - +
227A MET* 4.6 1.3 - - - +
228A HIS* 3.8 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 3.7 28.6 + - + +
221A ARG 3.6 7.5 + - - +
222A PHE* 3.3 8.8 + - - +
223A TYR 3.0 0.6 - - - -
224A ALA* 1.3 80.9 - - - +
226A ALA* 1.3 62.2 + - - +
227A MET 3.3 0.4 - - - -
228A HIS* 3.2 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PHE* 2.9 43.5 + - + +
223A TYR* 3.1 10.3 + - + -
225A ALA* 1.3 77.6 - - - +
227A MET* 1.3 60.0 + - - +
228A HIS* 3.3 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 3.7 23.1 - - - +
110A TRP* 3.6 30.7 - - + +
223A TYR* 2.7 43.5 + - + +
224A ALA* 4.6 1.8 - - - +
226A ALA* 1.3 72.7 - - - +
228A HIS* 1.3 63.2 + - - +
----------------------------------------------------------
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