Contacts of the helix formed by residues 316 - 326 (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 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A VAL* 4.0 3.1 - - + +
309A MET* 3.7 23.8 - - + +
315A SER* 1.3 70.7 - - - +
317A ASN* 1.3 74.8 + - - +
319A ALA* 3.4 1.2 + - - +
320A TYR* 2.9 28.8 + - - +
337A MET* 4.1 5.4 - - + +
340A LEU* 3.5 36.1 - - + +
341A LEU* 3.5 38.6 - - + +
344A GLU* 2.9 18.0 + - - +
501A MPD 3.2 41.7 - - + -
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Residues in contact with ASN 317 (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 SER* 3.2 7.2 + - - +
316A MET* 1.3 102.0 - - - +
318A ASP* 1.3 59.6 + - - +
320A TYR* 3.5 5.9 + - - +
321A ASP* 3.0 35.6 + - - +
341A LEU* 5.9 1.0 - - - +
344A GLU* 4.6 0.6 + - - -
501A MPD 3.6 10.9 - - - +
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Residues in contact with ASP 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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314A LEU* 3.9 25.9 - - + +
315A SER* 3.2 25.3 + - - +
317A ASN* 1.3 75.8 - - - +
319A ALA* 1.3 65.9 + - - +
321A ASP* 3.1 14.5 + - - +
322A ILE* 3.1 24.4 + - - +
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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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305A VAL* 3.7 14.8 - - + +
308A LEU* 3.4 23.5 - - + +
309A MET* 3.5 24.2 - - + +
314A LEU* 3.9 14.2 - - + +
315A SER 2.9 17.5 + - - +
316A MET 3.8 2.5 - - - +
318A ASP* 1.3 75.6 - - - +
320A TYR* 1.3 62.8 + - - +
322A ILE* 3.1 14.9 + - - +
323A VAL* 3.2 9.9 + - - +
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Residues in contact with TYR 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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301A VAL* 4.3 15.7 - - + -
305A VAL* 3.9 17.0 - - + +
316A MET 2.9 19.2 + - - +
317A ASN* 3.8 6.3 - - - +
319A ALA* 1.3 72.7 - - - +
321A ASP* 1.3 66.3 + - - +
323A VAL* 3.1 7.1 + - + +
324A LYS* 3.0 53.2 + - + +
330A ILE* 3.9 14.8 + - + +
332A PRO* 3.3 30.1 - - + +
501A MPD 3.6 51.4 - - + -
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Residues in contact with ASP 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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317A ASN* 3.0 21.5 + - - +
318A ASP* 3.1 17.1 + - - +
320A TYR* 1.3 77.7 - - - +
322A ILE* 1.3 62.2 + - - +
324A LYS* 3.2 27.2 + - - +
325A MET* 3.2 33.6 + - + +
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Residues in contact with ILE 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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210A ILE* 4.7 9.6 - - + +
211A LEU* 4.9 13.0 - - + -
308A LEU* 3.9 14.4 - - + -
312A LEU* 3.8 14.4 - - + -
314A LEU* 3.3 31.6 - - + -
318A ASP* 3.1 12.3 + - + +
319A ALA* 3.1 8.5 + - - +
321A ASP* 1.3 77.2 - - - +
323A VAL* 1.3 62.5 + - - +
325A MET* 3.1 40.2 + - + +
326A LYS* 3.6 9.3 + - + +
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Residues in contact with VAL 323 (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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210A ILE* 4.2 19.2 - - + +
216A LEU* 4.4 10.3 - - + -
301A VAL* 3.9 22.0 - - + -
304A THR* 4.2 8.7 - - + -
305A VAL* 4.0 17.9 - - + -
308A LEU* 3.6 17.5 - - + -
319A ALA 3.2 13.3 + - - +
320A TYR* 3.1 12.5 + - + +
322A ILE* 1.3 77.2 - - - +
324A LYS* 1.3 57.4 + - - +
325A MET 3.1 0.7 + - - -
326A LYS* 3.2 5.0 + - - +
327A LYS* 2.9 26.3 + - + +
330A ILE* 4.0 16.6 - - + -
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Residues in contact with LYS 324 (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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320A TYR* 3.0 49.5 + - + +
321A ASP* 3.2 32.0 + - - +
323A VAL* 1.3 73.8 - - - +
325A MET* 1.3 63.9 + - - +
327A LYS 3.9 8.3 - - - -
328A SER* 3.3 33.5 - - - +
330A ILE* 4.1 15.9 - - + +
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Residues in contact with MET 325 (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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321A ASP* 3.2 23.0 + - + +
322A ILE* 3.1 34.0 + - + +
323A VAL 3.1 0.8 - - - -
324A LYS* 1.3 78.8 - - - +
326A LYS* 1.3 72.0 + - + +
328A SER* 4.9 2.4 + - - -
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Residues in contact with LYS 326 (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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208A VAL* 3.3 17.6 - - + +
209A GLU* 3.6 23.8 + - - +
210A ILE* 3.0 47.8 + - + +
211A LEU* 4.8 3.4 - - - +
212A PRO* 5.8 1.4 - - - +
322A ILE* 3.9 13.0 - - + +
323A VAL 3.2 5.2 + - - +
325A MET* 1.3 88.9 - - + +
327A LYS* 1.3 58.1 + - - +
328A SER 3.9 1.1 - - - -
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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