Contacts of the helix formed by residues 258 - 274 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250I TYR* 3.4 18.3 - - - -
251I HIS 3.6 21.1 - - - +
252I ALA* 5.6 1.1 + - - +
254I VAL 2.8 21.4 + - - +
255I ALA 3.0 20.2 + - - -
256I TYR 2.7 15.1 + - - +
257I HIS* 1.3 73.9 - - - +
259I ASN* 1.3 71.8 + - - +
260I ILE* 2.8 40.8 + - - +
261I HIS* 3.0 6.9 + - - +
262I ALA 3.0 18.2 + - - -
429I TRP* 5.3 1.5 - - - -
432I ARG* 4.0 8.3 - - - +
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Residues in contact with ASN 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I ASN* 3.4 30.4 + - - +
214I PRO* 3.2 22.4 - - - +
215I LEU* 3.9 3.6 - - + +
247I GLU* 2.7 44.1 + - + +
250I TYR* 3.4 27.6 - - + +
251I HIS 5.2 0.7 - - - +
252I ALA* 5.8 2.8 - - - -
258I ASN* 1.3 79.3 - - - +
260I ILE* 1.3 60.7 + - - +
262I ALA* 3.6 6.4 - - - +
263I ALA* 2.9 28.4 + - - +
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Residues in contact with ILE 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I VAL* 3.8 26.6 - - + +
204I PHE* 4.0 15.3 - - + -
207I ALA* 4.2 21.5 - - + -
212I ASN* 4.7 7.0 - - - +
214I PRO* 4.1 9.9 - - + -
258I ASN* 2.8 20.2 + - - +
259I ASN* 1.3 78.2 - - - +
261I HIS* 1.3 61.1 + - - +
263I ALA* 3.2 2.6 + - - +
264I ASP* 2.8 28.6 + - - +
429I TRP* 3.8 17.3 - - + -
432I ARG* 3.7 30.7 - - - +
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Residues in contact with HIS 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I TYR* 3.1 59.8 + + - +
257I HIS* 4.3 6.5 - + - -
258I ASN* 3.0 7.7 + - - +
260I ILE* 1.3 78.9 - - - +
262I ALA* 1.3 62.5 + - - +
264I ASP* 3.0 7.9 + - - +
265I VAL* 2.9 39.6 + - + +
297I HIS* 3.1 11.9 + + - -
298I ASP* 3.2 21.1 - - + -
415I ASP* 2.9 19.9 + - - -
418I ASN* 5.2 2.4 + - - -
429I TRP* 3.7 16.3 - - + -
2017I ZN 2.3 25.2 - - - -
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Residues in contact with ALA 262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I LEU* 4.0 10.1 - - + -
250I TYR* 3.4 44.0 - - + +
258I ASN 3.0 6.5 + - - +
259I ASN* 3.6 8.3 - - - +
261I HIS* 1.3 77.9 - - - +
263I ALA* 1.3 63.1 + - - +
265I VAL* 3.3 2.4 + - - +
266I VAL* 3.0 27.4 + - - +
294I SER 4.3 1.2 - - - +
295I ALA 3.9 7.2 - - - +
297I HIS* 4.6 11.7 - - - -
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Residues in contact with ALA 263 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I VAL* 4.2 2.0 - - + -
214I PRO* 3.7 13.5 - - + -
215I LEU* 3.6 32.5 - - - +
218I ILE* 3.8 18.5 - - + +
259I ASN 2.9 20.2 + - - +
260I ILE 3.5 4.9 - - - +
262I ALA* 1.3 75.8 - - - +
264I ASP* 1.3 56.0 + - - +
266I VAL* 3.4 4.4 + - - +
267I GLN* 3.0 30.0 + - - +
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Residues in contact with ASP 264 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201I LEU 5.7 0.9 - - - +
203I VAL* 4.4 15.9 - - + +
260I ILE 2.8 12.9 + - - +
261I HIS* 3.3 12.0 + - - +
263I ALA* 1.3 74.9 - - - +
265I VAL* 1.3 62.3 + - + +
267I GLN* 3.2 9.4 + - - +
268I SER* 2.8 35.1 + - - -
417I SER* 4.4 2.2 + - - -
418I ASN* 3.3 25.6 + - - -
421I LYS* 3.0 26.6 + - - -
429I TRP* 3.5 25.2 + - + -
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Residues in contact with VAL 265 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261I HIS* 2.9 34.2 + - + +
262I ALA 3.9 2.0 - - - +
264I ASP* 1.3 77.1 - - + +
266I VAL* 1.3 59.0 + - - +
268I SER* 4.4 4.3 - - - -
269I THR* 2.9 35.7 + - - +
294I SER* 4.0 13.7 - - - +
297I HIS* 3.3 38.1 - - + +
411I VAL* 4.3 8.7 - - + +
414I ALA* 3.8 20.8 - - + +
415I ASP* 3.7 18.2 - - + +
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Residues in contact with VAL 266 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I LEU* 3.9 9.2 - - + -
218I ILE* 4.8 3.6 - - + -
219I MET* 3.5 25.4 - - + -
222I ILE* 3.8 17.9 - - + -
262I ALA 3.0 18.7 + - - +
263I ALA* 3.5 8.7 - - - +
265I VAL* 1.3 77.4 - - - +
267I GLN* 1.3 58.3 + - - +
269I THR* 3.2 4.3 + - - -
270I HIS* 2.9 27.0 + - - +
291I ILE* 4.1 11.9 - - + +
294I SER* 3.7 8.1 - - - -
295I ALA* 3.4 39.9 - - + +
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Residues in contact with GLN 267 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196I VAL* 2.8 33.2 + - + +
198I LYS 2.9 21.6 + - - -
199I TRP* 3.7 10.2 + - - +
201I LEU* 3.5 39.5 - - + +
203I VAL* 6.5 0.2 - - + -
218I ILE* 4.1 13.5 - - + -
222I ILE* 4.0 9.0 - - - -
263I ALA 3.0 17.7 + - - +
264I ASP* 3.2 10.4 + - - +
266I VAL* 1.3 78.2 - - - +
268I SER* 1.3 62.4 + - - +
270I HIS* 3.2 4.5 - - - +
271I VAL* 3.0 45.9 + - - +
421I LYS* 5.0 0.3 + - - -
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Residues in contact with SER 268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199I TRP* 3.6 22.6 - - - -
264I ASP* 2.8 18.1 + - - -
265I VAL* 4.4 0.2 - - - -
267I GLN* 1.3 76.6 + - - +
269I THR* 1.3 61.3 + - - +
271I VAL* 3.1 3.8 + - - +
272I LEU* 2.9 34.7 + - - +
414I ALA* 3.9 17.7 - - - -
417I SER* 3.7 7.0 + - - -
421I LYS* 3.0 27.2 + - - -
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Residues in contact with THR 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I VAL* 2.9 20.8 + - - +
266I VAL 3.5 3.6 - - - -
268I SER* 1.3 75.2 - - - +
270I HIS* 1.3 58.6 + - - +
272I LEU* 3.3 7.4 + - - +
273I LEU* 2.8 49.3 + - + +
290I ALA* 4.1 19.1 - - + +
291I ILE* 4.5 3.6 - - + +
294I SER* 2.8 27.2 + - - +
410I MET* 4.3 6.3 - - - -
411I VAL* 3.9 11.4 - - + +
414I ALA* 3.4 16.1 - - - +
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Residues in contact with HIS 270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196I VAL* 3.4 24.1 - - + +
197I ASN* 2.8 27.7 + - - +
222I ILE* 3.3 39.6 - - + +
225I GLU* 4.1 11.3 - - + +
226I ARG* 2.9 70.9 + - + +
266I VAL 2.9 13.2 + - - +
267I GLN 3.2 9.0 - - - +
268I SER 3.1 0.2 - - - -
269I THR* 1.3 78.9 - - - +
271I VAL* 1.3 64.1 + - + +
273I LEU* 3.5 7.0 + - - -
274I SER* 3.4 8.0 + - - -
291I ILE* 5.0 3.6 - - + -
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Residues in contact with VAL 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196I VAL 4.0 2.7 - - - +
197I ASN* 3.8 27.6 - - - +
198I LYS 4.0 4.0 - - - +
199I TRP* 3.7 29.8 - - + +
267I GLN* 3.0 38.6 + - - +
268I SER 3.1 6.3 + - - +
270I HIS* 1.3 75.3 - - - +
272I LEU* 1.3 66.9 + - + +
274I SER* 3.0 19.8 + - - -
275I THR* 3.5 5.4 + - - -
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Residues in contact with LEU 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199I TRP* 4.0 18.2 - - + -
268I SER 2.9 20.1 + - - +
269I THR 3.7 3.6 - - - +
271I VAL* 1.3 76.2 - - + +
273I LEU* 1.3 63.8 + - - +
275I THR* 3.0 31.7 + - - +
410I MET* 3.7 46.0 - - + +
413I CYS* 4.1 5.6 - - + -
414I ALA* 4.1 10.3 - - + +
478I TRP* 4.0 28.5 - - + -
481I TRP* 4.1 19.5 - - + +
489I ALA* 6.4 0.2 - - + -
492I ILE* 4.5 8.1 - - + -
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Residues in contact with LEU 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226I ARG* 3.5 17.0 - - - +
269I THR* 2.8 25.7 + - + +
271I VAL 3.2 0.4 - - - -
272I LEU* 1.3 76.2 - - - +
274I SER* 1.3 59.5 + - - +
275I THR 3.2 4.9 + - - +
278I LEU* 4.3 14.0 - - - +
282I PHE* 4.3 14.7 - - + -
287I ILE* 3.8 32.5 - - + +
290I ALA* 4.4 3.4 - - + -
291I ILE* 3.8 31.4 - - + -
407I LEU* 4.1 16.8 - - + -
410I MET* 3.5 28.7 - - + -
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Residues in contact with SER 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197I ASN* 6.6 0.2 - - - -
226I ARG* 2.9 22.7 + - - +
270I HIS* 3.4 8.2 + - - -
271I VAL* 3.0 15.4 + - - -
273I LEU* 1.3 76.6 - - - +
275I THR* 1.3 65.3 - - - +
276I PRO* 3.3 5.7 - - - +
279I 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
------------------------------------------------------------
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