Contacts of the helix formed by residues 312 - 322 (chain A) in PDB entry 1MPX
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 TRP 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ILE* 4.7 1.6 - - + -
202A ASP* 3.9 21.1 - - + +
205A MSE 3.4 43.7 - - + -
206A GLY* 3.5 30.9 + - - +
207A ASP* 3.1 11.1 + - - +
212A TYR* 3.8 26.5 - + - -
287A ASP* 3.2 23.5 + - - -
288A LYS* 6.1 2.5 - - - -
311A MSE 1.3 79.5 - - - +
313A GLY* 1.3 69.3 + - - +
314A ALA 3.8 0.9 - - - -
315A ILE* 3.5 2.3 - - - +
316A HIS* 2.8 71.1 + + + -
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Residues in contact with GLY 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PRO 3.8 6.5 - - - -
201A ILE* 3.3 33.9 - - - -
207A ASP* 3.0 12.6 + - - -
310A ASP 4.1 1.9 + - - -
311A MSE 3.7 1.2 - - - -
312A TRP* 1.3 76.4 - - - +
314A ALA* 1.3 62.7 + - - +
316A HIS* 3.9 1.0 - - - +
317A SER* 2.8 29.1 + - - -
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Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PRO* 4.1 11.9 - - + +
301A TRP* 3.6 19.1 - - + +
302A LEU 3.3 42.6 - - - +
303A GLN* 3.3 18.2 + - + +
310A ASP 5.0 1.4 + - - -
313A GLY* 1.3 73.1 - - - +
315A ILE* 1.3 57.9 + - - +
317A SER* 3.8 0.5 - - - -
318A TYR* 2.9 31.4 + - - +
333A LEU* 4.8 2.2 - - + -
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Residues in contact with ILE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A GLN* 3.0 19.3 + - - +
311A MSE 3.9 8.5 - - - +
312A TRP 3.5 11.9 - - - +
314A ALA* 1.3 75.4 - - - +
316A HIS* 1.3 76.7 + - + +
318A TYR* 3.5 8.2 + - + +
319A ALA* 3.1 23.7 + - + +
333A LEU* 3.9 31.4 - - + +
335A MSE 4.2 14.6 - - + -
404A TRP* 4.0 16.8 - - + +
405A PRO* 6.1 0.7 - - + -
573A THR* 3.8 20.6 - - - +
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Residues in contact with HIS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP* 3.8 15.4 - - + +
312A TRP* 2.8 88.9 + + + +
313A GLY 4.1 0.9 - - - +
315A ILE* 1.3 87.2 - - + +
317A SER* 1.3 60.2 + - - +
319A ALA* 3.4 6.1 + - - +
320A ALA* 3.1 26.9 + - - +
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 3.4 29.5 - - - +
287A ASP* 3.9 9.5 - - - +
290A MSE 4.5 4.5 - - - +
301A TRP* 3.5 33.7 - - - -
313A GLY 2.8 20.8 + - - -
316A HIS* 1.3 74.4 - - - +
318A TYR* 1.3 66.5 + - - +
320A ALA* 3.2 14.4 + - - +
321A MSE 3.4 17.8 + - - +
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Residues in contact with TYR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A TRP* 3.6 18.3 - - + +
314A ALA 2.9 19.0 + - - +
315A ILE* 3.7 11.0 - - + +
317A SER* 1.3 77.2 - - - +
319A ALA* 1.3 62.5 + - + +
321A MSE 3.2 1.6 + - - -
322A GLU* 3.0 70.2 + - + +
331A ASN* 3.0 26.1 + - - +
332A TYR 3.4 24.5 - - - -
333A LEU* 3.7 41.1 - - + -
387A PRO 4.6 0.6 + - - -
388A VAL* 3.7 16.9 - - + +
402A LYS 5.0 0.7 + - - -
403A ALA* 4.6 2.9 - - - -
404A TRP 3.8 24.9 + - - -
638A CA 4.3 1.4 - - - -
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ILE* 3.1 16.5 + - + +
316A HIS* 3.8 8.1 - - + +
317A SER 3.3 0.2 - - - -
318A TYR* 1.3 86.8 - - + +
320A ALA* 1.3 62.1 + - - +
322A GLU* 4.6 3.6 - - - +
323A PRO* 3.3 20.8 - - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ASP* 3.4 26.9 - - + +
290A MSE 4.4 2.0 - - + -
291A ALA* 3.7 20.2 - - + +
316A HIS 3.1 14.3 + - - +
317A SER* 3.2 13.4 + - - +
319A ALA* 1.3 76.7 - - - +
321A MSE 1.3 58.9 + - - +
323A PRO* 4.4 3.6 - - - +
324A ARG* 3.3 17.3 + - - -
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Residues in contact with MSE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 5.8 3.4 - - + -
290A MSE 3.7 46.7 - - + +
293A THR* 3.6 31.2 - - + +
294A PRO 4.4 3.8 - - - +
295A LEU* 3.4 35.9 - - + +
299A THR* 5.5 6.5 - - - +
301A TRP* 3.8 23.1 - - - -
317A SER 3.6 9.2 - - - +
318A TYR 3.2 1.6 + - - -
320A ALA* 1.3 81.0 - - - +
322A GLU* 1.3 62.7 + - - +
323A PRO* 3.4 4.0 - - - -
324A ARG* 3.1 20.2 + - - +
331A ASN* 3.7 18.2 - - - +
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Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A TYR* 3.0 45.4 + - + +
319A ALA* 4.6 2.7 - - - +
321A MSE 1.3 76.8 - - - +
323A PRO* 1.3 68.7 - - + +
325A ASP* 3.0 24.6 + - - +
328A ASN* 3.1 11.6 + - - +
331A ASN* 3.0 24.1 + - - +
402A LYS 4.7 3.1 - - - +
403A ALA* 5.8 2.0 - - + +
404A TRP 5.6 1.6 - - - +
638A CA 2.5 31.1 - - - -
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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