Contacts of the helix formed by residues 257 - 273 (chain N) in PDB entry 5L4K
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 SER 257 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221N ILE* 5.4 0.2 - - - +
256N ALA* 1.3 76.1 - - - +
258N GLN* 1.3 73.7 + - - +
259N GLN* 3.4 15.3 - - - -
260N PHE* 3.5 6.8 + - - +
261N LEU* 3.2 28.0 + - - +
754N HIS* 3.7 12.2 + - - -
756N HIS* 5.0 1.2 - - - -
757N MET* 3.6 39.1 + - - +
758N PRO* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 258 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253N TYR* 5.8 3.9 + - + -
256N ALA 4.8 2.8 + - - -
257N SER* 1.3 85.3 - - - +
259N GLN* 1.3 59.5 + - - +
261N LEU* 3.5 15.2 + - + +
262N SER* 3.0 34.2 + - - +
452N ASN* 2.3 59.3 + - + +
453N HIS* 5.9 3.1 - - + +
486N MET 4.6 7.8 - - - +
487N GLY* 5.2 9.5 - - - +
488N THR* 6.1 2.5 - - + -
756N HIS* 6.3 0.6 - - - +
757N MET* 5.5 1.8 - - - +
758N PRO* 3.9 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 259 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257N SER* 4.4 9.8 - - - -
258N GLN* 1.3 76.6 - - - +
260N PHE* 1.3 62.3 + - + +
262N SER* 4.0 7.2 - - - -
263N SER* 3.0 24.1 + - - -
487N GLY 4.2 18.6 + - - +
521N LEU 5.7 0.8 + - - -
522N GLY* 4.2 19.2 + - - -
523N SER* 4.0 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 260 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220N LEU 3.5 22.0 - - - -
221N ILE* 4.4 7.9 - - + -
224N ASP* 3.7 35.9 - - + -
225N ASP 4.2 0.7 - - - -
226N PRO* 3.8 37.5 - - + -
229N VAL* 4.0 20.6 - - + -
252N LEU* 4.0 17.9 - - + -
256N ALA* 4.1 23.1 - - + -
257N SER* 3.5 11.8 + - - +
258N GLN 3.2 0.6 - - - -
259N GLN* 1.3 82.1 - - + +
261N LEU* 1.3 60.4 + - + +
262N SER 3.1 1.3 - - - -
263N SER* 3.0 19.4 + - - +
264N VAL* 3.0 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252N LEU* 3.7 27.8 - - + +
253N TYR* 3.6 38.8 - - + +
256N ALA* 4.7 1.3 - - + +
257N SER 3.2 22.4 + - - +
258N GLN* 4.0 14.4 - - + +
260N PHE* 1.3 77.2 - - + +
262N SER* 1.3 57.8 + - - +
264N VAL* 3.6 9.0 - - + +
265N ILE* 3.2 30.9 - - - +
329N LEU* 3.5 47.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 262 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258N GLN* 3.0 19.4 + - - +
259N GLN* 4.5 6.7 - - - -
260N PHE 3.1 0.2 - - - -
261N LEU* 1.3 78.2 - - - +
263N SER* 1.3 59.3 + - - +
264N VAL 3.4 0.2 - - - -
265N ILE* 3.8 14.8 - - - +
266N GLN* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 263 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226N PRO* 3.7 26.8 - - - +
259N GLN 3.0 15.9 + - - -
260N PHE* 3.0 10.8 + - - -
262N SER* 1.3 78.6 - - - +
264N VAL* 1.3 59.3 + - - +
266N GLN* 3.5 10.1 + - - +
267N ASN* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226N PRO* 4.0 15.0 - - + +
229N VAL* 3.6 31.0 - - + -
230N SER* 4.4 8.1 - - - -
233N LEU* 6.5 0.4 - - + -
252N LEU* 5.0 7.2 - - + -
260N PHE* 3.0 23.3 + - + +
261N LEU* 3.6 16.6 - - + +
263N SER* 1.3 73.9 - - - +
265N ILE* 1.3 69.3 + - - +
266N GLN 3.1 1.1 - - - -
267N ASN* 3.0 9.4 + - - +
268N LEU* 2.9 28.6 + - + +
329N LEU* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261N LEU 3.2 22.7 - - - +
262N SER* 3.8 17.7 - - - +
264N VAL* 1.3 76.0 - - - +
266N GLN* 1.3 60.0 + - + +
268N LEU* 3.4 3.6 + - - -
269N ARG* 2.9 37.9 + - - +
326N ILE* 3.7 30.1 - - + -
329N LEU* 3.7 33.2 - - + +
330N SER* 4.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 266 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262N SER 3.2 19.7 - - - +
263N SER* 3.5 8.7 + - - +
264N VAL 3.1 0.2 - - - -
265N ILE* 1.3 81.5 - - + +
267N ASN* 1.3 77.2 + - - +
269N ARG* 3.2 7.2 + - + +
270N THR* 2.6 57.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 267 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226N PRO* 3.7 25.8 - - - +
227N GLN* 3.7 14.4 + - - +
230N SER* 3.6 21.8 - - - +
263N SER* 2.8 25.4 + - - +
264N VAL* 3.0 6.9 + - - +
266N GLN* 1.3 90.6 + - - +
268N LEU* 1.3 58.7 + - - +
270N THR* 3.5 5.9 + - - +
271N VAL* 3.0 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230N SER* 4.2 14.6 - - - +
233N LEU* 5.1 11.0 - - + -
234N GLU* 3.3 42.6 - - + +
264N VAL* 2.9 19.7 + - + +
265N ILE* 3.7 7.0 - - - +
267N ASN* 1.3 76.8 - - - +
269N ARG* 1.3 79.2 + - - +
271N VAL* 4.2 8.8 - - + +
272N GLY* 2.9 21.5 + - - -
325N MET* 5.4 5.6 - - + -
326N ILE* 4.1 20.2 - - + -
329N LEU* 4.6 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 269 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265N ILE* 2.9 35.8 + - - +
266N GLN* 3.2 9.1 + - + +
268N LEU* 1.3 102.9 + - - +
270N THR* 1.3 60.7 + - - +
272N GLY* 3.7 3.6 - - - +
273N THR* 2.8 32.8 + - - +
323N LEU* 3.8 25.4 - - - +
326N ILE* 3.6 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 270 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266N GLN* 2.6 34.9 + - - -
267N ASN* 4.0 7.4 - - - -
269N ARG* 1.3 76.8 - - - +
271N VAL* 1.3 62.1 + - + +
273N THR* 3.7 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230N SER* 5.8 0.2 - - - +
231N ASP* 5.1 10.3 - - - +
234N GLU* 5.7 9.0 - - + -
267N ASN* 3.0 24.6 + - + +
268N LEU* 4.2 9.0 - - + +
270N THR* 1.3 74.9 - - + +
272N GLY* 1.3 65.0 + - - +
273N THR 3.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 272 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268N LEU 2.9 20.5 + - - -
269N ARG* 3.3 7.1 + - - -
271N VAL* 1.3 74.4 - - - +
273N THR* 1.3 63.7 + - - +
274N PRO* 3.4 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 273 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269N ARG* 2.8 21.7 + - - +
270N THR* 3.7 14.6 + - - +
271N VAL 3.1 12.4 - - - +
272N GLY* 1.3 75.7 - - - +
274N PRO* 1.3 82.3 - - + +
----------------------------------------------------------
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