Contacts of the helix formed by residues 314 - 320 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309C LEU* 2.7 51.5 + - - +
312C THR* 3.2 8.6 - - - -
313C ASN* 1.3 81.3 - - - +
315C GLU* 1.3 64.2 + - - +
316C LEU* 3.7 3.4 + - - +
317C ALA* 3.1 17.5 + - - +
318C LEU* 3.1 20.8 + - - +
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Residues in contact with GLU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ASN 3.8 3.0 + - - +
314C SER* 1.3 75.3 - - - +
316C LEU* 1.3 57.0 + - - +
318C LEU* 3.4 26.7 + - - +
319C MET* 3.0 28.6 + - - +
336D LYS* 3.8 22.4 + - - +
339D GLN* 4.4 4.3 + - - +
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C PRO* 5.5 4.9 - - + -
309C LEU* 4.5 17.0 - - + -
314C SER* 3.1 8.4 - - - +
315C GLU* 1.3 80.7 - - - +
317C ALA* 1.3 56.9 + - - +
319C MET* 3.3 7.9 - - + +
320C TYR* 3.1 43.3 + - + -
325C VAL* 3.5 19.6 - - + +
326C LEU* 4.7 5.6 - - + -
329C HIS* 3.7 49.8 - - + +
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Residues in contact with ALA 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C LEU 3.3 19.7 - - - +
310C ILE* 3.8 4.9 - - - +
313C ASN* 5.0 1.3 - - - -
314C SER* 3.1 24.2 + - - +
316C LEU* 1.3 74.6 - - - +
318C LEU* 1.3 61.1 + - - +
321C ASN 2.9 23.4 + - - -
322C ASP* 3.0 23.7 + - - +
325C VAL* 3.7 19.0 - - + +
358D ARG* 3.2 5.1 + - - -
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ASN 5.4 2.9 - - - +
314C SER 3.1 12.2 + - - +
315C GLU* 3.5 32.1 - - - +
317C ALA* 1.3 77.9 - - - +
319C MET* 1.3 64.3 + - - +
321C ASN* 3.5 15.2 + - - +
332D ALA* 4.0 28.5 - - + +
335D PHE* 4.5 14.8 - - + -
336D LYS* 4.5 12.1 - - + +
339D GLN* 3.4 30.5 - - - +
358D ARG* 3.5 16.7 + - - +
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Residues in contact with MET 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C GLU 3.0 17.9 + - - +
316C LEU* 3.3 11.0 - - + +
318C LEU* 1.3 81.5 - - - +
320C TYR* 1.3 83.4 - - + +
321C ASN* 3.4 5.6 + - - -
319D MET* 3.2 32.1 - - - +
320D TYR* 3.1 50.4 + - + +
329D HIS* 6.0 1.6 - - - +
332D ALA* 4.3 12.2 - - + +
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Residues in contact with TYR 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C LEU* 3.1 35.8 + - + +
319C MET* 1.3 90.6 - - + +
321C ASN* 1.3 75.0 + - - +
322C ASP 3.2 1.6 - - - -
323C SER* 2.9 22.7 + - - +
325C VAL* 3.7 29.8 - - + -
328C ASN* 3.6 30.9 + - + -
329C HIS* 4.0 17.4 + - - -
332C ALA* 3.7 13.5 - - - +
319D MET* 2.9 42.6 + - + +
320D TYR* 3.8 25.4 - + - -
328D ASN* 4.4 5.3 - - - +
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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