Contacts of the helix formed by residues 305 - 312 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301H HIS* 5.5 0.4 - - - -
304H VAL* 1.3 75.5 - - - +
306H ASN* 1.3 66.9 + - - +
307H GLN* 3.5 10.2 + - - +
308H PHE* 3.0 18.0 + - - +
309H LEU* 3.0 22.7 + - - +
326H LEU* 4.2 3.8 - - - -
440H GLN* 3.0 25.3 + - - -
452H SER* 5.4 0.5 + - - -
3008H ZAR 6.1 0.7 - - - -
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Residues in contact with ASN 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H SER* 1.3 72.2 - - - +
307H GLN* 1.3 58.1 + - - +
309H LEU* 3.1 8.1 + - - +
310H ILE* 2.9 42.2 + - + +
324H SER* 4.3 3.4 - - - +
325H VAL* 3.4 15.1 - - + +
326H LEU* 2.8 41.7 + - - +
327H GLU* 2.9 31.5 + - - -
369H ASP* 4.0 11.5 + - - -
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Residues in contact with GLN 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H SER* 3.1 9.1 + - - +
306H ASN* 1.3 80.1 - - - +
308H PHE* 1.3 56.5 + - - +
310H ILE* 3.2 21.2 + - - +
311H ASN* 2.8 71.4 + - - +
452H SER* 6.0 2.5 - - - +
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Residues in contact with PHE 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304H VAL* 3.5 23.3 - - + -
305H SER* 3.0 25.9 + - - +
307H GLN* 1.3 75.7 - - - +
309H LEU* 1.3 60.9 + - + +
310H ILE 3.2 0.3 + - - -
311H ASN* 3.2 5.5 + - - +
312H THR* 2.8 64.4 + - + +
440H GLN* 3.8 14.4 - - + +
443H ARG* 3.3 51.4 - - + -
444H GLU* 3.6 39.0 - - + -
447H ARG* 4.1 8.1 - - - -
449H MET* 4.3 7.4 - - + -
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Residues in contact with LEU 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302H PRO* 4.5 5.6 - - + -
304H VAL* 3.8 22.2 - - + -
305H SER 3.0 14.4 + - - +
306H ASN* 3.5 8.3 - - - +
308H PHE* 1.3 80.4 - - + +
310H ILE* 1.3 59.9 + - - +
312H THR* 3.5 4.2 + - - +
313H ASN 3.5 1.4 + - - -
314H SER* 2.7 55.4 + - - +
316H LEU* 4.5 10.5 - - + -
317H ALA* 3.4 6.4 - - + +
325H VAL* 4.1 16.8 - - + -
326H LEU* 3.7 39.3 - - + -
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Residues in contact with ILE 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306H ASN* 2.9 30.6 + - + +
307H GLN* 3.5 23.8 - - - +
309H LEU* 1.3 76.4 - - - +
311H ASN* 1.3 67.0 + - - +
313H ASN* 3.0 20.3 + - - +
317H ALA* 3.9 9.8 - - + +
322H ASP* 3.6 59.7 - - + +
325H VAL* 4.3 5.2 - - + -
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Residues in contact with ASN 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355E GLN* 5.6 1.9 - - - +
307H GLN* 2.8 58.4 + - - +
308H PHE* 3.9 1.2 - - - +
310H ILE* 1.3 75.7 - - - +
312H THR* 1.3 58.5 + - - +
313H ASN* 3.1 13.6 + - - +
444H GLU* 5.7 1.2 + - - -
449H MET* 3.8 26.6 - - + +
452H SER* 6.0 0.2 + - - -
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Residues in contact with THR 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308H PHE* 2.8 56.3 + - + +
309H LEU* 3.5 11.4 + - - +
311H ASN* 1.3 75.2 - - - +
313H ASN* 1.3 73.1 + - - +
314H SER* 3.2 8.3 + - - -
447H ARG* 4.1 15.3 - - - +
449H MET* 3.7 23.8 - - + -
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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