Contacts of the helix formed by residues 258 - 274 (chain G) in PDB entry 1MKD
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 258 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G TYR* 3.4 18.0 - - - -
251G HIS 3.6 21.8 - - - +
252G ALA* 5.6 0.9 + - - +
254G VAL 2.7 22.7 + - - +
255G ALA 2.9 21.8 + - - -
256G TYR 2.7 11.6 + - - +
257G HIS* 1.3 73.0 - - - +
259G ASN* 1.3 67.4 + - - +
260G ILE* 2.8 41.1 + - - +
261G HIS* 3.0 6.8 + - - +
262G ALA 3.0 22.2 + - - -
429G TRP* 5.3 0.9 - - - -
432G ARG* 4.0 7.9 - - - +
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Residues in contact with ASN 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G ASN* 3.4 31.0 + - - +
214G PRO* 3.2 21.8 - - - +
215G LEU* 4.0 4.3 - - + +
247G GLU* 2.7 42.3 + - + +
250G TYR* 3.5 27.7 - - + +
251G HIS 5.2 0.9 - - - +
252G ALA* 5.8 2.8 - - - -
258G ASN* 1.3 77.0 - - - +
260G ILE* 1.3 63.4 + - - +
261G HIS 3.3 0.2 - - - -
262G ALA* 3.7 5.6 - - - +
263G ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203G VAL* 3.8 21.6 - - + +
204G PHE* 4.0 15.9 - - + -
207G ALA* 4.2 25.1 - - + -
212G ASN* 4.7 6.7 - - - +
214G PRO* 4.1 10.5 - - + -
258G ASN* 2.8 19.9 + - - +
259G ASN* 1.3 77.5 - - - +
261G HIS* 1.3 61.3 + - - +
263G ALA* 3.2 2.8 + - - +
264G ASP* 2.8 28.9 + - - +
429G TRP* 3.8 16.8 - - + -
432G ARG* 3.7 31.6 - - - +
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Residues in contact with HIS 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256G TYR* 3.1 58.5 + + + +
257G HIS* 4.3 6.1 - + - -
258G ASN* 3.0 7.3 + - - +
260G ILE* 1.3 79.5 - - - +
262G ALA* 1.3 63.1 + - - +
264G ASP* 2.9 8.1 + - - +
265G VAL* 2.9 39.6 + - + +
297G HIS* 3.0 11.4 + + - -
298G ASP* 3.2 20.2 - - + -
415G ASP* 3.0 20.7 + - - -
418G ASN* 5.2 2.2 + - - -
429G TRP* 3.7 16.9 - - + -
2013G ZN 2.3 24.7 - - - -
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Residues in contact with ALA 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G LEU* 4.0 9.2 - - + -
250G TYR* 3.4 44.0 - - + +
258G ASN 3.0 6.2 + - - +
259G ASN* 3.7 8.3 - - - +
261G HIS* 1.3 78.2 - - - +
263G ALA* 1.3 63.3 + - - +
265G VAL* 3.3 2.3 + - - +
266G VAL* 3.0 27.0 + - - +
294G SER 4.3 0.6 - - - +
295G ALA 3.9 7.6 - - - +
297G HIS* 4.5 12.8 - - - -
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Residues in contact with ALA 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203G VAL* 4.2 2.2 - - + -
214G PRO* 3.7 13.7 - - + -
215G LEU* 3.6 32.9 - - - +
218G ILE* 3.8 18.6 - - + +
259G ASN 2.9 20.3 + - - +
260G ILE 3.4 4.3 - - - +
262G ALA* 1.3 75.6 - - - +
264G ASP* 1.3 58.2 + - - +
266G VAL* 3.4 4.1 + - - +
267G GLN* 3.0 30.1 + - - +
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Residues in contact with ASP 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G LEU 5.7 1.0 - - - +
203G VAL* 4.4 15.2 - - + +
260G ILE 2.8 13.7 + - - +
261G HIS* 2.9 10.8 + - - +
263G ALA* 1.3 74.3 - - - +
265G VAL* 1.3 61.9 + - + +
267G GLN* 3.3 10.2 + - - +
268G SER* 2.8 34.6 + - - -
417G SER* 4.4 2.3 + - - -
418G ASN* 3.3 25.6 + - - -
421G LYS* 3.0 26.1 + - - -
429G TRP* 3.4 26.4 + - + -
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Residues in contact with VAL 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G HIS* 2.9 34.4 + - + +
262G ALA 3.9 2.5 - - - +
264G ASP* 1.3 78.2 - - + +
266G VAL* 1.3 57.6 + - - +
268G SER* 4.4 4.9 - - - -
269G THR* 2.9 34.8 + - - -
294G SER* 4.0 16.4 - - - +
297G HIS* 3.3 37.0 - - + +
411G VAL* 4.3 8.7 - - + +
414G ALA* 3.8 21.5 - - + +
415G ASP* 3.7 17.7 - - + +
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Residues in contact with VAL 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G LEU* 3.9 9.6 - - + -
218G ILE* 4.7 4.0 - - + -
219G MET* 3.5 24.7 - - + -
222G ILE* 3.8 17.7 - - + -
262G ALA 3.0 19.5 + - - +
263G ALA* 3.5 9.0 - - - +
265G VAL* 1.3 77.0 - - - +
267G GLN* 1.3 58.8 + - - +
269G THR* 3.1 4.2 + - - -
270G HIS* 2.9 27.0 + - - +
291G ILE* 4.1 12.1 - - + +
294G SER* 3.8 7.4 - - - -
295G ALA* 3.4 38.8 - - + +
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Residues in contact with GLN 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G VAL* 2.8 32.6 + - + +
198G LYS 2.9 21.4 + - - -
199G TRP 3.8 10.0 - - - +
201G LEU* 3.4 40.0 - - + +
203G VAL* 6.5 0.4 - - + -
218G ILE* 4.1 13.0 - - + -
222G ILE* 3.9 9.4 - - - -
263G ALA 3.0 18.5 + - - +
264G ASP* 3.3 10.4 + - - +
266G VAL* 1.3 75.1 - - - +
268G SER* 1.3 64.5 + - - +
270G HIS* 3.1 4.3 - - - +
271G VAL* 3.0 47.7 + - - +
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Residues in contact with SER 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G TRP* 3.6 23.6 - - - -
264G ASP* 2.8 18.5 + - - -
265G VAL* 3.9 4.0 - - - -
267G GLN* 1.3 76.8 + - - +
269G THR* 1.3 60.9 + - - +
271G VAL* 3.2 1.4 + - - -
272G LEU* 2.9 34.0 + - - +
414G ALA* 3.9 15.0 - - - -
417G SER* 3.7 6.8 + - - -
421G LYS* 3.1 27.2 + - - -
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Residues in contact with THR 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G VAL* 2.9 19.2 + - - +
266G VAL 3.5 4.0 - - - -
268G SER* 1.3 76.2 - - - +
270G HIS* 1.3 58.4 + - - +
272G LEU* 3.2 7.1 + - - +
273G LEU* 2.8 47.5 + - + +
290G ALA* 4.1 19.7 - - + +
291G ILE* 4.5 3.6 - - + +
294G SER* 2.8 26.8 + - - +
410G MET* 4.4 6.3 - - + -
411G VAL* 4.0 11.9 - - + +
414G ALA* 3.4 16.1 - - - +
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Residues in contact with HIS 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G VAL* 3.4 24.8 - - - +
197G ASN* 2.8 27.2 + - - -
222G ILE* 3.4 39.1 - - + +
225G GLU* 4.1 11.6 - - + +
226G ARG* 2.8 69.9 + - + +
266G VAL 2.9 13.1 + - - +
267G GLN 3.1 9.4 - - - +
269G THR* 1.3 79.2 - - - +
271G VAL* 1.3 62.5 + - - +
273G LEU* 3.4 6.9 + - - -
274G SER* 3.4 8.8 + - - -
291G ILE* 4.9 4.2 - - + +
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Residues in contact with VAL 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G VAL 4.0 4.3 - - - +
197G ASN* 3.8 25.1 - - - +
198G LYS 4.0 4.5 - - - +
199G TRP* 3.7 30.5 - - + +
267G GLN* 3.0 38.9 + - - +
268G SER 3.6 5.8 - - - +
270G HIS* 1.3 74.3 - - - +
272G LEU* 1.3 68.2 + - + +
274G SER* 3.0 20.1 + - - -
275G THR* 3.5 5.7 + - - -
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Residues in contact with LEU 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G TRP* 4.0 14.1 - - + -
268G SER 2.9 19.5 + - - +
269G THR* 3.7 4.0 - - - +
271G VAL* 1.3 79.2 - - + +
273G LEU* 1.3 64.0 + - - +
275G THR* 3.0 31.8 + - - +
410G MET* 3.7 45.3 - - + +
413G CYS* 4.2 3.8 - - + -
414G ALA* 4.2 13.0 - - + +
478G TRP* 4.0 32.5 - - + -
481G TRP* 4.0 20.4 - - + +
489G ALA* 6.4 0.2 - - + -
492G ILE* 4.6 7.0 - - + -
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Residues in contact with LEU 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226G ARG* 3.5 16.4 - - - +
269G THR* 2.8 27.0 + - + +
270G HIS* 4.6 0.2 - - - -
271G VAL 3.2 0.4 - - - -
272G LEU* 1.3 77.7 - - - +
274G SER* 1.3 59.8 + - - +
275G THR 3.2 4.9 + - - +
278G LEU* 4.3 14.2 - - - +
282G PHE* 4.2 15.5 - - + -
287G ILE* 3.8 39.9 - - + +
290G ALA* 4.4 3.1 - - + -
291G ILE* 3.8 24.0 - - + -
407G LEU* 4.1 16.4 - - + -
410G MET* 3.5 27.8 - - + -
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Residues in contact with SER 274 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G ARG* 2.9 22.4 + - - +
270G HIS* 3.4 9.0 + - - -
271G VAL* 3.0 14.2 + - - -
273G LEU* 1.3 77.7 - - - +
275G THR* 1.3 67.4 + - - +
276G PRO* 3.3 5.2 - - - +
279G GLU* 5.7 0.5 - - - +
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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
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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) + - + + + + + -
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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