Contacts of the helix formed by residues 314 - 320 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309J LEU* 2.7 50.1 + - - +
312J THR* 3.2 8.3 - - - -
313J ASN* 1.3 82.7 - - - +
315J GLU* 1.3 65.0 + - - +
316J LEU* 3.7 4.6 + - - +
317J ALA* 3.1 18.0 + - - +
318J LEU* 3.0 20.3 + - - +
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Residues in contact with GLU 315 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336I LYS* 3.6 22.7 + - - +
339I GLN* 4.8 2.6 + - - +
313J ASN 3.8 3.2 + - - +
314J SER* 1.3 73.6 - - - +
316J LEU* 1.3 57.2 + - - +
318J LEU* 3.3 26.9 + - - +
319J MET* 2.9 30.1 + - - +
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Residues in contact with LEU 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319I MET* 6.3 0.7 - - + -
302J PRO* 5.5 4.9 - - + -
309J LEU* 4.6 17.0 - - + -
314J SER* 3.1 8.4 - - - +
315J GLU* 1.3 81.3 - - - +
317J ALA* 1.3 55.6 + - - +
319J MET* 3.3 7.8 - - + +
320J TYR* 3.1 43.6 + - + -
325J VAL* 3.5 20.5 - - + +
326J LEU* 4.7 6.5 - - + -
329J HIS* 3.7 50.5 - - + +
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Residues in contact with ALA 317 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358I ARG* 3.3 3.5 + - - -
309J LEU 3.4 19.5 - - - +
310J ILE* 3.9 4.9 - - - +
313J ASN* 5.0 1.3 - - - -
314J SER* 3.1 24.0 + - - +
316J LEU* 1.3 75.9 - - - +
318J LEU* 1.3 60.3 + - - +
321J ASN 3.0 23.9 + - - -
322J ASP* 3.1 25.7 + - - +
325J VAL* 3.7 19.0 - - + +
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Residues in contact with LEU 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332I ALA* 3.6 31.5 - - + +
335I PHE* 4.7 7.6 - - + -
336I LYS* 3.8 28.3 - - + +
339I GLN* 3.6 22.7 - - - +
358I ARG* 4.0 10.4 + - - +
313J ASN 5.4 2.2 - - - +
314J SER 3.0 12.2 + - - +
315J GLU* 3.5 33.9 - - - +
317J ALA* 1.3 77.7 - - - +
319J MET* 1.3 64.9 + - - +
321J ASN* 3.5 15.2 + - - +
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Residues in contact with MET 319 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316I LEU* 6.3 0.9 - - + -
319I MET* 2.9 36.1 - - - +
320I TYR* 2.6 51.2 + - + +
329I HIS* 5.6 4.0 - - + +
332I ALA* 4.0 9.8 - - + +
315J GLU 2.9 17.4 + - - +
316J LEU* 3.3 11.2 - - + +
318J LEU* 1.3 80.3 - - - +
320J TYR* 1.3 84.3 + - + +
321J ASN* 3.4 5.1 + - - -
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Residues in contact with TYR 320 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319I MET* 2.6 46.3 + - + +
320I TYR* 3.6 26.9 - + - -
328I ASN* 4.2 4.2 - - - +
316J LEU* 3.1 37.3 + - + +
319J MET* 1.3 89.3 - - + +
321J ASN* 1.3 74.3 + - - +
322J ASP 3.2 2.0 - - - -
323J SER* 2.9 28.4 + - - +
325J VAL* 3.7 21.1 - - + -
328J ASN* 3.5 31.4 + - + +
329J HIS* 4.0 17.5 + - - -
332J ALA* 3.7 12.8 - - - +
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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