Contacts of the helix formed by residues 305 - 312 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301E HIS* 5.5 0.7 - - - -
304E VAL* 1.3 76.3 - - - +
306E ASN* 1.3 64.1 + - - +
307E GLN* 3.5 10.3 + - - +
308E PHE* 3.0 18.5 + - - +
309E LEU* 3.0 22.3 + - - +
326E LEU* 4.2 4.0 - - - -
440E GLN* 2.9 25.4 + - - -
452E SER* 5.4 0.7 + - - -
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Residues in contact with ASN 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305E SER* 1.3 74.0 - - - +
307E GLN* 1.3 59.6 + - - +
309E LEU* 3.1 8.1 + - - +
310E ILE* 2.8 41.0 + - + +
324E SER* 4.2 3.8 - - - +
325E VAL* 3.4 15.8 - - + +
326E LEU* 2.8 40.9 + - - +
327E GLU* 3.0 30.3 + - - -
369E ASP* 4.0 11.9 + - - -
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Residues in contact with GLN 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305E SER* 3.5 9.1 + - - +
306E ASN* 1.3 79.4 - - - +
308E PHE* 1.3 57.2 + - - +
310E ILE* 3.2 20.8 + - - +
311E ASN* 2.8 70.3 + - - +
452E SER* 6.0 2.7 - - - +
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Residues in contact with PHE 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E VAL* 3.5 22.0 - - + -
305E SER* 3.0 25.7 + - - +
307E GLN* 1.3 73.9 - - - +
309E LEU* 1.3 62.9 + - + +
310E ILE 3.2 0.3 + - - -
311E ASN* 3.2 6.4 + - - +
312E THR* 2.8 64.6 + - + +
440E GLN* 3.8 14.6 - - + +
443E ARG* 3.4 51.4 - - + -
444E GLU* 3.6 39.3 - - + -
447E ARG* 4.0 9.0 - - - -
449E MET* 4.3 7.0 - - + -
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Residues in contact with LEU 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302E PRO* 4.6 6.1 - - + -
304E VAL* 3.8 22.7 - - + -
305E SER 3.0 16.4 + - - +
306E ASN* 3.4 8.1 - - - +
308E PHE* 1.3 79.4 - - + +
310E ILE* 1.3 59.3 + - - +
312E THR* 3.5 3.8 + - - +
313E ASN 3.5 0.9 + - - -
314E SER* 2.7 55.0 + - - +
316E LEU* 4.5 10.5 - - + -
317E ALA* 3.3 7.4 - - + +
325E VAL* 4.1 16.6 - - + -
326E LEU* 3.6 38.8 - - + -
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Residues in contact with ILE 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E ASN* 2.8 30.2 + - + +
307E GLN* 3.6 22.7 - - - +
308E PHE 3.1 0.2 - - - -
309E LEU* 1.3 77.2 - - - +
311E ASN* 1.3 65.5 + - - +
313E ASN* 3.1 19.6 + - - +
317E ALA* 3.9 10.0 - - + +
322E ASP* 3.5 59.3 - - + +
325E VAL* 4.3 5.2 - - + -
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Residues in contact with ASN 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E GLN* 2.8 58.1 + - - +
308E PHE* 3.8 1.3 - - - +
310E ILE* 1.3 75.6 - - - +
312E THR* 1.3 58.3 + - - +
313E ASN* 3.1 12.6 + - - +
444E GLU* 5.7 1.0 + - - -
449E MET* 3.8 26.6 - - + +
452E SER* 6.0 0.6 + - - -
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Residues in contact with THR 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308E PHE* 2.8 60.9 + - + +
309E LEU* 3.5 11.4 + - - +
311E ASN* 1.3 75.2 - - - +
313E ASN* 1.3 72.4 + - - +
314E SER* 3.2 8.1 + - - -
447E ARG* 4.1 16.2 - - - +
449E MET* 3.8 19.3 - - + -
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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