Contacts of the helix formed by residues 417 - 421 (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 417 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199J TRP* 3.9 17.0 - - - -
264J ASP* 4.4 1.7 + - - -
268J SER* 3.7 4.2 + - - -
413J CYS 3.3 8.5 - - - -
414J ALA* 2.8 23.7 + - - -
415J ASP 3.4 1.2 + - - -
416J LEU* 1.3 76.5 - - - +
418J ASN* 1.3 70.1 + - - +
419J PRO* 3.4 3.1 - - - -
420J THR* 2.7 31.9 + - - -
421J LYS* 3.4 23.7 + - - +
478J TRP* 3.9 5.2 - - - +
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Residues in contact with ASN 418 (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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256J TYR* 2.5 40.6 + - - -
261J HIS* 5.4 2.6 + - - -
264J ASP* 3.3 24.7 + - - -
415J ASP 5.2 2.7 + - - -
416J LEU 3.5 0.4 - - - -
417J SER* 1.3 79.8 + - - +
419J PRO* 1.3 59.3 - - + +
420J THR 2.9 5.9 + - - -
421J LYS* 3.0 18.4 + - - +
426J TYR* 3.4 16.6 - - + +
429J TRP* 3.5 28.2 - - + +
3010J ZAR 3.0 26.4 - - - -
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Residues in contact with PRO 419 (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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416J LEU 4.0 11.7 - - - +
417J SER 3.6 3.1 - - - -
418J ASN* 1.3 94.7 - - + +
420J THR* 1.3 55.0 + - - +
421J LYS 3.4 0.4 - - - -
426J TYR* 3.5 38.4 - - + +
469J PHE* 4.1 18.6 - - + -
470J ILE* 4.0 6.1 - - + -
474J VAL* 4.1 8.3 - - + -
496J LEU* 3.5 31.9 - - + +
499J ASN* 2.8 24.2 + - - +
3010J ZAR 3.6 7.6 - - - -
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Residues in contact with THR 420 (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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199J TRP* 3.3 34.2 + - - -
417J SER* 2.7 20.0 + - - +
419J PRO* 1.3 77.0 - - - +
421J LYS* 1.3 61.2 + - - +
422J PRO* 4.8 0.2 - - - +
474J VAL* 4.4 2.7 - - + -
478J TRP* 3.6 37.7 - - + +
492J ILE* 3.4 20.5 - - + +
495J THR* 3.4 19.7 + - - +
496J LEU* 3.9 23.6 - - + +
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Residues in contact with LYS 421 (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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199J TRP* 3.4 59.3 + - + +
200J GLY* 4.6 1.3 - - - -
264J ASP* 3.0 31.3 + - - -
267J GLN* 5.0 0.8 + - - -
268J SER* 3.0 19.7 + - - -
417J SER* 3.4 23.5 + - - +
418J ASN* 3.0 15.4 + - - +
420J THR* 1.3 79.9 - - - +
422J PRO* 1.4 79.9 - - + +
425J LEU* 4.2 17.7 - - + +
426J TYR* 4.1 1.5 - - - +
429J TRP* 5.4 3.6 - - + +
495J THR* 3.7 2.8 - - - +
499J ASN* 2.9 21.1 + - - -
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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