Contacts of the helix formed by residues 314 - 320 (chain G) 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 SER 314 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309G LEU* 2.7 50.3 + - - +
312G THR* 3.2 8.5 - - - -
313G ASN* 1.3 82.4 - - - +
315G GLU* 1.3 65.2 + - - +
316G LEU* 3.7 3.9 + - - -
317G ALA* 3.1 17.7 + - - +
318G LEU* 3.0 20.8 + - - +
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Residues in contact with GLU 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F LYS* 3.1 28.7 + - - +
339F GLN* 3.9 7.3 + - - +
313G ASN 3.8 3.2 + - - +
314G SER* 1.3 74.6 - - - +
316G LEU* 1.3 58.6 + - - +
318G LEU* 3.3 25.5 + - - +
319G MET* 2.9 28.9 + - - +
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Residues in contact with LEU 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302G PRO* 5.5 4.7 - - + -
309G LEU* 4.5 16.6 - - + -
314G SER* 3.1 8.0 - - - +
315G GLU* 1.3 80.4 - - - +
317G ALA* 1.3 56.6 + - - +
319G MET* 3.3 7.6 - - + +
320G TYR* 3.1 44.7 + - + -
325G VAL* 3.6 19.9 - - + +
326G LEU* 4.7 6.3 - - + -
329G HIS* 3.7 50.0 - - + +
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Residues in contact with ALA 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358F ARG* 3.0 9.2 + - - -
309G LEU 3.4 20.2 - - - +
310G ILE* 3.9 5.4 - - - +
313G ASN* 5.0 1.3 - - - -
314G SER* 3.1 23.9 + - - +
316G LEU* 1.3 73.6 - - - +
318G LEU* 1.3 60.7 + - - +
321G ASN 2.9 25.3 + - - -
322G ASP* 3.1 18.8 + - - +
325G VAL* 3.8 18.8 - - + +
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Residues in contact with LEU 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332F ALA* 3.6 28.9 - - + +
335F PHE* 4.2 12.6 - - + -
336F LYS* 4.1 23.8 - - + +
339F GLN* 3.1 33.0 - - - +
358F ARG* 3.5 13.8 + - - +
313G ASN 5.5 2.7 - - - +
314G SER 3.0 12.6 + - - +
315G GLU* 3.5 26.7 - - - +
317G ALA* 1.3 77.6 - - - +
319G MET* 1.3 65.6 + - - +
321G ASN* 3.5 15.2 + - - +
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Residues in contact with MET 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F MET* 3.4 29.4 - - - +
320F TYR* 2.9 49.1 + - + +
329F HIS* 5.7 3.1 - - + +
332F ALA* 3.9 13.3 - - + +
315G GLU 2.9 17.6 + - - +
316G LEU* 3.3 10.8 - - + +
318G LEU* 1.3 80.9 - - - +
320G TYR* 1.3 82.4 + - + +
321G ASN* 3.4 5.8 + - - -
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Residues in contact with TYR 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F MET* 3.0 47.9 + - + +
320F TYR* 3.7 26.0 - + - -
328F ASN* 4.4 4.3 - - - +
316G LEU* 3.1 37.2 + - + +
319G MET* 1.3 90.2 - - + +
321G ASN* 1.3 74.8 + - - +
322G ASP 3.2 1.8 - - - -
323G SER* 3.0 28.4 + - - +
325G VAL* 3.7 21.5 - - + -
328G ASN* 3.5 29.3 + - + -
329G HIS* 4.0 18.3 + - - -
332G ALA* 3.7 11.3 - - - +
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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