Contacts of the helix formed by residues 215 - 224 (chain A) in PDB entry 4KM9
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 ASN 215 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ALA 4.1 0.3 - - - +
214A TRP* 1.3 90.2 + - - +
216A GLY* 1.3 60.8 + - - +
217A GLN* 4.4 8.3 - - + +
218A GLY* 2.8 35.8 + - - -
219A ILE* 3.7 17.8 + - - +
262A ASP* 2.9 37.8 + - - +
263A GLY 4.8 1.0 + - - -
265A ASN* 3.2 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLY* 3.3 29.9 + - - -
160A HIS* 6.3 0.2 - - - -
178A LEU* 3.9 9.9 - - - +
211A ALA* 4.1 11.0 + - - -
214A TRP 3.8 0.6 + - - -
215A ASN* 1.3 72.6 - - - +
217A GLN* 1.3 60.4 + - - +
219A ILE* 3.4 4.3 + - - +
220A LEU* 3.1 30.9 + - - +
265A ASN* 4.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER* 3.1 50.4 + - - +
158A GLY* 4.1 1.5 - - - -
180A THR* 4.9 1.2 + - - -
181A GLU* 5.4 1.6 + - - -
215A ASN* 3.4 6.9 - - + +
216A GLY* 1.3 77.3 - - - +
218A GLY* 1.3 57.4 + - - +
220A LEU* 3.3 19.1 + - - +
221A GLU* 2.9 32.9 + - - +
224A ARG* 4.5 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TRP* 3.7 25.2 - - - -
215A ASN* 2.8 25.3 + - - -
217A GLN* 1.3 71.4 - - - +
219A ILE* 1.3 58.3 + - - +
221A GLU* 3.3 10.0 + - - +
222A LEU* 3.1 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 5.2 5.8 - - + -
203A VAL* 5.9 0.4 - - + -
207A GLU* 4.1 18.8 - - + +
210A SER* 3.6 22.9 - - - -
211A ALA* 3.8 29.8 - - + +
214A TRP* 3.7 21.1 - - + -
215A ASN 3.7 7.4 + - - +
216A GLY 3.4 8.6 + - - +
217A GLN 3.3 0.4 - - - -
218A GLY* 1.3 73.6 - - - +
220A LEU* 1.3 60.2 + - - +
222A LEU* 3.1 22.5 + - + +
223A LEU* 3.0 39.8 + - + +
244A ILE* 5.2 7.0 - - + -
245A PHE* 4.9 3.1 - - + -
255A VAL* 4.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLY* 4.2 4.5 - - - -
178A LEU* 4.1 26.0 - - + -
179A LEU 3.8 11.7 - - - +
180A THR* 3.6 36.3 - - + +
201A VAL* 4.5 6.5 - - + -
216A GLY 3.1 19.6 + - - +
217A GLN* 3.3 31.2 - - - +
219A ILE* 1.3 77.6 - - - +
221A GLU* 1.3 60.5 + - - +
223A LEU* 3.2 15.2 + - + +
224A ARG* 3.1 39.2 + - - +
234A LEU* 3.9 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 2.9 16.7 + - - +
218A GLY* 3.4 13.0 - - - +
220A LEU* 1.3 75.8 - - - +
222A LEU* 1.3 63.1 + - + +
224A ARG* 3.2 43.3 + - - +
225A THR* 3.6 13.2 - - - +
254A ARG* 4.3 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TRP* 4.2 8.1 - - + -
218A GLY 3.1 16.9 + - - +
219A ILE* 3.1 22.7 + - + +
221A GLU* 1.3 74.8 - - - +
223A LEU* 1.3 62.6 + - - +
224A ARG 3.1 0.2 - - - -
225A THR* 2.6 26.9 + - - -
226A VAL* 3.7 7.6 + - - +
244A ILE* 4.6 11.2 - - + -
245A PHE* 4.7 5.6 - - + -
251A LEU* 4.3 26.7 - - + +
254A ARG* 3.4 44.2 - - + +
255A VAL* 3.7 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 5.4 1.1 - - + -
201A VAL* 4.4 16.2 - - + -
203A VAL* 3.9 24.5 - - + -
207A GLU* 3.4 24.0 - - - +
219A ILE* 3.0 24.2 + - + +
220A LEU* 3.2 18.6 + - + +
222A LEU* 1.3 76.8 - - - +
224A ARG* 1.3 56.4 + - - +
225A THR 3.3 0.2 + - - -
226A VAL* 3.0 25.7 + - - +
229A ALA* 3.8 25.1 - - + -
230A GLY* 3.4 4.5 - - - +
231A GLY 3.2 6.9 + - - -
234A LEU* 3.7 12.1 - - + -
240A ARG* 4.7 7.2 - - - +
244A ILE* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A THR* 3.2 25.5 + - - -
181A GLU 5.2 2.0 + - - -
217A GLN* 4.5 3.0 + - - -
220A LEU* 3.1 16.6 + - - +
221A GLU* 3.2 64.0 + - - +
222A LEU 3.1 0.6 - - - -
223A LEU* 1.3 77.2 - - - +
225A THR* 1.3 61.0 + - + +
231A GLY* 3.4 15.9 - - - +
232A PRO* 3.4 41.2 + - + +
234A LEU* 3.7 26.4 - - + +
----------------------------------------------------------
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