Contacts of the helix formed by residues 337 - 345 (chain A) in PDB entry 1MKP
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 MET 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A MET* 4.1 2.4 - - + +
334A PHE* 3.2 42.9 + - + +
336A PHE* 1.3 76.8 - - - +
338A GLY* 1.3 59.5 + - - +
340A LEU* 3.2 1.2 + - - +
341A LEU* 2.9 45.1 + - + +
501A MPD 3.7 41.4 - - + +
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Residues in contact with GLY 338 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A PHE 4.8 0.6 + - - -
335A ASN 5.1 1.6 + - - -
336A PHE* 3.3 0.8 - - - +
337A MET* 1.3 80.4 - - - +
339A GLN* 1.3 57.2 + - - +
341A LEU* 3.9 8.3 - - - +
342A ASP* 3.0 28.9 + - - +
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Residues in contact with GLN 339 (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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266A GLN 4.0 8.4 - - - +
267A ASN* 3.3 20.5 - - - +
268A LEU 2.9 31.0 + - - +
269A SER* 3.0 31.3 + - - +
272A PHE* 4.8 4.9 - - + -
335A ASN 4.3 6.8 + - - +
336A PHE* 3.3 36.8 + - + +
338A GLY* 1.3 75.2 - - - +
340A LEU* 1.3 61.3 + - - +
342A ASP* 3.7 6.0 - - - +
343A PHE* 2.9 28.5 + - - +
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Residues in contact with LEU 340 (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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272A PHE* 4.0 19.7 - - + -
302A THR* 3.8 30.5 - - + +
305A VAL* 4.0 14.4 - - + -
306A ALA* 4.1 5.6 - - + +
309A MET* 3.6 25.7 - - - +
316A MET* 3.5 19.2 - - + +
336A PHE 3.0 12.6 + - - +
339A GLN* 1.3 75.1 - - - +
341A LEU* 1.3 60.7 + - - +
343A PHE* 3.3 4.5 + - + +
344A GLU* 3.0 26.7 + - - +
501A MPD 3.2 44.6 - - + -
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Residues in contact with LEU 341 (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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316A MET* 3.5 28.7 - - + -
317A ASN* 5.9 1.3 - - - +
337A MET* 2.9 31.7 + - + +
338A GLY* 3.9 7.6 - - - +
340A LEU* 1.3 76.5 - - - +
342A ASP* 1.3 62.4 + - - +
344A GLU* 3.1 33.5 - - - +
345A ARG* 3.5 13.3 + - - +
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Residues in contact with ASP 342 (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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269A SER* 5.6 1.9 + - - -
338A GLY 3.0 18.7 + - - +
339A GLN* 3.7 7.6 - - - +
341A LEU* 1.3 75.7 - - - +
343A PHE* 1.3 64.6 + - - +
345A ARG* 3.1 38.9 + - - +
346A THR* 3.6 6.6 + - - -
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Residues in contact with PHE 343 (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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269A SER* 5.3 3.6 - - - -
272A PHE* 3.7 33.7 - + + -
273A PRO* 5.8 2.0 - - + -
276A ILE* 4.1 11.4 - - + -
306A ALA* 3.5 30.3 - - + -
309A MET* 3.8 25.6 - - + -
310A GLN* 3.3 31.0 - - + -
339A GLN 2.9 19.7 + - - +
340A LEU* 3.5 4.0 - - + +
342A ASP* 1.3 74.9 + - - +
344A GLU* 1.3 64.9 + - - +
346A THR* 3.1 36.3 + - + -
347A LEU* 3.7 17.7 - - + +
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Residues in contact with GLU 344 (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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309A MET* 3.7 15.2 - - + +
314A LEU 5.3 0.9 - - - +
315A SER* 3.7 18.3 - - - -
316A MET* 2.9 34.2 + - - +
317A ASN 4.6 0.3 + - - -
340A LEU 3.0 11.7 + - - +
341A LEU* 3.1 26.7 - - - +
343A PHE* 1.3 79.0 - - - +
345A ARG* 1.3 60.7 + - + +
347A LEU* 3.1 22.5 + - + +
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Residues in contact with ARG 345 (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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341A LEU* 3.8 10.6 + - - +
342A ASP* 3.1 31.0 + - - +
344A GLU* 1.3 77.1 - - + +
346A THR* 1.3 62.0 + - - +
347A LEU 3.1 11.0 + - - +
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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