Contacts of the helix formed by residues 417 - 421 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199D TRP* 3.9 17.5 - - - -
264D ASP* 4.4 1.6 + - - -
268D SER* 3.6 4.0 + - - -
413D CYS 3.3 8.5 - - - -
414D ALA* 2.8 24.5 + - - -
415D ASP 3.4 1.0 - - - -
416D LEU* 1.3 75.5 - - - +
418D ASN* 1.3 71.3 + - - +
419D PRO* 3.4 3.4 - - - -
420D THR* 2.7 31.8 + - - -
421D LYS* 3.4 25.3 + - - +
478D TRP* 3.9 5.4 - - - +
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Residues in contact with ASN 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D TYR* 2.5 40.8 + - - -
261D HIS* 5.4 2.4 + - - -
264D ASP* 3.3 24.7 + - - -
415D ASP 5.3 2.8 + - - -
416D LEU* 3.6 0.6 - - - -
417D SER* 1.3 79.2 + - - +
419D PRO* 1.3 62.3 - - + +
420D THR 2.9 5.7 + - - -
421D LYS* 3.0 18.7 + - - +
426D TYR* 3.4 18.0 - - + +
429D TRP* 3.4 28.7 - - + +
3004D ZAR 3.1 23.2 - - - -
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Residues in contact with PRO 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416D LEU 4.0 11.7 - - - +
417D SER 3.6 2.7 - - - -
418D ASN* 1.3 93.4 - - + +
420D THR* 1.3 55.2 + - - +
421D LYS 3.4 0.2 - - - -
426D TYR* 3.5 39.9 - - + +
469D PHE* 4.1 18.2 - - + -
470D ILE* 4.0 5.8 - - + -
474D VAL* 4.2 8.3 - - + -
496D LEU* 3.4 30.5 - - + +
499D ASN* 2.8 23.8 + - - +
3004D ZAR 3.7 8.1 - - - -
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Residues in contact with THR 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D TRP* 3.3 33.4 + - - -
417D SER* 2.7 20.5 + - - +
419D PRO* 1.3 79.6 - - - +
421D LYS* 1.3 60.8 + - - +
474D VAL* 4.4 2.5 - - + -
478D TRP* 3.6 37.0 - - + +
492D ILE* 3.4 21.7 - - + +
495D THR* 3.4 19.1 + - - +
496D LEU* 3.9 24.5 - - + +
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Residues in contact with LYS 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D TRP* 3.3 59.8 + - + +
200D GLY* 4.7 1.3 - - - -
264D ASP* 2.9 31.1 + - - -
267D GLN* 5.0 1.0 + - - -
268D SER* 3.1 19.2 + - - -
417D SER* 3.4 22.1 + - - +
418D ASN* 3.0 16.5 + - - +
420D THR* 1.3 80.5 - - - +
422D PRO* 1.3 82.0 - - + +
423D LEU* 4.1 0.2 - - - -
425D LEU* 4.2 16.5 - - + +
426D TYR* 4.1 0.9 - - - +
429D TRP* 5.4 3.1 - - + +
495D THR* 3.6 2.3 - - - +
499D ASN* 2.9 20.4 + - - -
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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