Contacts of the helix formed by residues 292 - 304 (chain H) in PDB entry 1MK9
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 ILE 292 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750G ALA 5.9 1.6 - - - +
209H PRO* 5.7 13.2 - - + +
212H LEU* 3.3 23.6 - - + -
290H SER* 3.1 6.5 - - - +
291H GLU* 1.3 103.0 - - + +
293H GLU* 1.3 66.0 + - - +
294H ALA 3.3 1.6 - - - -
295H LYS* 3.3 16.9 + - + +
296H VAL* 3.2 24.3 + - + +
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Residues in contact with GLU 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H MET* 3.3 31.6 - - + +
290H SER* 3.3 24.3 + - - +
292H ILE* 1.3 79.3 - - - +
294H ALA* 1.3 56.8 + - - +
296H VAL* 3.2 9.7 + - - +
297H ARG* 3.0 61.2 + - + +
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Residues in contact with ALA 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H TYR* 4.0 17.4 - - + +
244H GLN* 4.1 10.5 - - + -
245H ILE* 3.4 26.0 - - + -
289H MET* 3.6 22.6 - - - -
290H SER 3.3 10.2 + - - +
291H GLU 4.7 0.2 - - - +
293H GLU* 1.3 78.3 - - - +
295H LYS* 1.3 59.6 + - - +
297H ARG* 3.2 2.7 + - - +
298H TYR* 2.8 31.2 + - - +
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Residues in contact with LYS 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H PRO 5.5 0.6 + - - -
212H LEU* 3.9 15.0 - - + -
213H ASN* 2.5 39.8 + - + +
216H TYR* 3.7 24.6 - - + -
245H ILE* 3.7 33.3 - - + +
291H GLU* 3.1 37.9 + - - +
292H ILE* 3.6 19.9 - - + +
294H ALA* 1.3 77.4 - - - +
296H VAL* 1.3 62.3 + - - +
298H TYR* 3.1 4.7 + - - +
299H VAL* 2.9 30.8 + - - +
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Residues in contact with VAL 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746G LEU* 3.2 42.1 - - + +
747G TYR* 4.7 4.9 - - + -
212H LEU* 3.5 23.8 - - + -
292H ILE* 3.2 15.7 + - + +
293H GLU* 3.4 10.1 - - - +
295H LYS* 1.3 80.5 - - - +
297H ARG* 1.3 60.2 + - + +
299H VAL* 3.5 1.9 + - - +
300H LYS* 3.1 47.5 + - + +
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Residues in contact with ARG 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373F TYR* 4.5 25.5 - - - +
241H TYR* 3.7 28.4 + - + +
289H MET* 3.3 39.7 - - - +
293H GLU* 3.0 39.7 + - + +
294H ALA 3.2 4.2 + - - +
296H VAL* 1.3 79.2 - - + +
298H TYR* 1.3 60.5 + - - +
300H LYS* 3.9 7.2 - - + +
301H LEU* 3.0 28.1 + - - +
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Residues in contact with TYR 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216H TYR* 3.7 26.9 - + + -
219H ALA* 4.3 7.2 - - + -
220H ARG* 3.4 43.0 + - + +
223H ILE* 3.7 17.7 - - + +
224H LEU* 5.6 0.7 - - - +
238H PHE* 3.3 58.9 - + + +
241H TYR* 3.7 20.8 - - + -
242H GLN* 4.5 7.8 + - + -
294H ALA 2.8 17.3 + - - +
295H LYS* 3.4 8.7 - - - +
297H ARG* 1.3 75.1 - - - +
299H VAL* 1.3 70.1 + - - +
301H LEU* 3.0 5.6 + - - +
302H ALA* 2.9 19.7 + - + -
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Residues in contact with VAL 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746G LEU* 4.5 8.3 - - + -
212H LEU* 4.6 5.8 - - + -
215H LEU* 3.9 22.0 - - + +
216H TYR* 3.8 31.2 - - + +
219H ALA* 4.8 7.2 - - + -
295H LYS 2.9 22.5 + - - +
296H VAL 4.0 3.4 - - - +
298H TYR* 1.3 79.1 - - + +
300H LYS* 1.3 61.0 + - - +
302H ALA* 3.4 6.1 + - + +
303H ARG* 3.1 54.5 + - + +
308H TYR* 5.5 2.9 - - + +
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Residues in contact with LYS 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F ASN* 3.6 35.7 + - - +
370F PHE* 3.2 21.6 + - - +
371F GLY 5.7 0.7 - - - -
372F ASP* 3.3 20.4 + - - +
746G LEU* 4.5 6.1 - - + -
747G TYR* 2.8 31.3 + - - -
296H VAL* 3.1 30.1 + - + +
297H ARG* 3.9 7.4 - - + +
299H VAL* 1.3 75.2 - - - +
301H LEU* 1.3 67.6 + - - +
303H ARG* 3.2 8.6 + - - +
304H SER* 3.0 24.1 + - - -
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Residues in contact with LEU 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D MET* 6.4 0.4 - - - -
234H LYS* 4.3 19.1 - - + +
237H GLU* 3.4 47.3 - - + +
238H PHE* 3.4 30.5 - - + -
241H TYR* 4.3 9.2 - - + -
297H ARG 3.0 17.6 + - - +
298H TYR 3.0 5.5 + - - +
300H LYS* 1.3 78.4 - - - +
302H ALA* 1.3 60.1 + - - +
304H SER* 2.5 28.8 + - - +
305H LEU* 3.5 10.5 - - + +
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Residues in contact with ALA 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H ALA* 4.2 22.4 - - + -
223H ILE* 4.7 5.6 - - + -
228H HIS* 3.3 17.0 - - + +
238H PHE* 3.7 18.1 - - + -
298H TYR* 2.9 12.4 + - + +
299H VAL 3.6 9.0 - - - +
301H LEU* 1.3 77.2 - - - +
303H ARG* 1.3 61.3 + - - +
305H LEU* 3.3 10.1 + - - +
308H TYR* 3.2 24.1 - - + +
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Residues in contact with ARG 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352F SER* 5.2 9.7 + - - +
354F THR* 2.7 52.8 + - - +
355F ASN* 3.0 26.6 + - - +
744G ASN* 5.6 1.0 + - - -
746G LEU* 3.2 12.3 - - - +
215H LEU* 3.8 35.4 - - - +
299H VAL* 3.1 31.2 + - + +
300H LYS* 3.2 5.4 + - - +
302H ALA* 1.3 70.7 - - - +
304H SER* 1.3 55.8 + - - +
305H LEU 2.7 26.5 + - - +
308H TYR* 3.6 42.5 + - + +
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Residues in contact with SER 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352F SER* 5.7 2.9 + - - -
355F ASN* 6.0 0.4 - - - +
300H LYS 3.0 11.9 + - - -
301H LEU* 2.5 35.1 + - - +
303H ARG* 1.3 75.3 - - - +
305H LEU* 1.3 62.2 + - - +
306H LYS* 3.7 2.3 + - - +
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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
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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