Contacts of the helix formed by residues 305 - 312 (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 305 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301G HIS* 5.5 0.9 - - - -
304G VAL* 1.3 75.5 - - - +
306G ASN* 1.3 64.9 + - - +
307G GLN* 3.6 9.6 + - - +
308G PHE* 3.0 18.2 + - - +
309G LEU* 3.1 22.2 + - - +
326G LEU* 4.2 4.0 - - - -
440G GLN* 3.0 24.3 + - - -
452G SER* 5.4 0.3 + - - -
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Residues in contact with ASN 306 (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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305G SER* 1.3 73.1 - - - +
307G GLN* 1.3 65.2 + - - +
309G LEU* 3.1 8.1 + - - +
310G ILE* 2.9 35.7 + - + +
324G SER* 4.2 3.2 - - - +
325G VAL* 3.4 14.5 - - + +
326G LEU* 2.8 41.9 + - - +
327G GLU* 2.9 30.5 + - - -
369G ASP* 4.0 12.5 + - - -
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Residues in contact with GLN 307 (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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305G SER* 3.2 9.7 + - - +
306G ASN* 1.3 79.9 - - - +
308G PHE* 1.3 57.4 + - - +
310G ILE* 3.2 20.3 + - - +
311G ASN* 2.8 71.2 + - - +
452G SER* 6.0 2.9 - - - +
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Residues in contact with PHE 308 (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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304G VAL* 3.5 22.7 - - + -
305G SER* 3.0 25.4 + - - +
307G GLN* 1.3 77.2 - - - +
309G LEU* 1.3 60.7 + - + +
311G ASN* 3.2 5.1 + - - +
312G THR* 2.8 65.5 + - + +
440G GLN* 3.7 14.3 - - + +
443G ARG* 3.3 51.1 - - + -
444G GLU* 3.6 39.5 - - + -
447G ARG* 4.1 8.3 - - - -
449G MET* 4.3 7.2 - - + -
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Residues in contact with LEU 309 (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* 4.5 5.4 - - + -
304G VAL* 3.8 23.1 - - + -
305G SER 3.1 15.5 + - - +
306G ASN* 3.5 8.5 - - - +
308G PHE* 1.3 79.2 - - + +
310G ILE* 1.3 59.1 + - - +
312G THR* 3.5 3.8 + - - +
313G ASN 3.4 1.2 + - - -
314G SER* 2.7 55.5 + - - +
316G LEU* 4.5 11.4 - - + -
317G ALA* 3.4 6.9 - - + +
325G VAL* 4.1 16.8 - - + -
326G LEU* 3.6 38.8 - - + -
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Residues in contact with ILE 310 (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* 5.8 0.4 - - - +
306G ASN* 2.9 28.2 + - + +
307G GLN* 3.6 24.2 - - - +
309G LEU* 1.3 77.7 - - - +
311G ASN* 1.3 61.5 + - - +
313G ASN* 3.0 24.8 + - - +
317G ALA* 3.9 9.6 - - + +
322G ASP* 3.5 59.1 - - + +
325G VAL* 4.3 6.1 - - + -
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Residues in contact with ASN 311 (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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351F LYS* 5.6 7.4 + - - +
355F GLN* 5.2 6.8 - - - +
307G GLN* 2.8 54.8 + - - +
308G PHE* 3.8 1.5 - - - +
310G ILE* 1.3 77.6 - - - +
312G THR* 1.3 60.2 + - - +
313G ASN* 3.1 11.4 + - - +
444G GLU* 5.7 1.0 + - - -
449G MET* 3.8 26.6 - - + +
452G SER* 6.0 0.2 + - - -
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Residues in contact with THR 312 (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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308G PHE* 2.8 55.4 + - + +
309G LEU* 3.5 11.3 + - - +
311G ASN* 1.3 76.2 - - - +
313G ASN* 1.3 72.9 + - - +
314G SER* 3.2 8.3 + - - -
447G ARG* 4.1 16.8 - - - +
449G MET* 3.7 24.2 - - + -
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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