Contacts of the helix formed by residues 354 - 360 (chain B) in PDB entry 5DK3
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 354 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B PRO* 1.3 75.9 - - - +
355B GLN* 1.3 65.4 + - - +
356B GLU* 3.2 15.6 + - - +
357B GLU* 3.1 17.7 + - - +
358B MET* 3.4 10.9 + - - +
349G TYR* 3.7 31.1 - - - +
350G THR 3.7 15.2 + - - -
351G LEU* 3.4 28.8 - - - +
352G PRO* 6.3 0.9 - - - -
439G LYS* 5.9 0.2 - - - -
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Residues in contact with GLN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B PRO 3.5 1.8 + - - -
354B SER* 1.3 73.0 + - - +
356B GLU* 1.3 78.1 + - - +
358B MET* 3.2 27.4 + - + +
359B THR* 4.3 4.3 + - - +
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Residues in contact with GLU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B SER* 3.2 10.9 + - - +
355B GLN* 1.3 98.2 + - - +
357B GLU* 1.3 59.3 + - - +
358B MET 3.3 0.2 - - - -
359B THR* 3.1 30.6 + - - +
360B LYS* 5.1 0.3 - - - +
349G TYR* 3.9 10.3 + - + -
439G LYS* 3.9 31.0 - - - +
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Residues in contact with GLU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B PRO* 3.7 13.8 - - + +
354B SER* 3.1 16.1 + - - +
356B GLU* 1.3 73.2 - - - +
358B MET* 1.3 56.4 + - - +
359B THR 3.1 4.9 - - - -
360B LYS* 2.9 28.4 + - + +
362B GLN 4.2 8.3 - - - +
363B VAL* 3.8 8.3 - - - +
364B SER* 2.7 53.5 + - - +
349G TYR* 3.6 36.6 - - + +
368G LEU* 4.8 2.0 - - - +
370G LYS* 2.8 24.6 + - - +
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Residues in contact with MET 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B PRO* 4.0 12.8 - - + +
354B SER 3.4 14.8 + - - +
355B GLN* 3.2 17.5 + - + +
357B GLU* 1.3 74.8 - - - +
359B THR* 1.4 52.1 + - - +
360B LYS 3.3 0.7 - - - -
363B VAL* 3.9 20.9 - - - -
414B LYS* 2.8 34.9 + - + +
417B TRP* 3.9 31.9 - - + +
418B GLN* 4.0 26.4 + - + +
443B LEU* 5.6 5.6 - - + -
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B GLN 4.7 4.5 - - - +
356B GLU* 3.1 25.1 + - - +
358B MET* 1.4 76.0 - - + +
360B LYS* 1.3 69.2 + - - +
414B LYS* 3.7 6.9 + - - +
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Residues in contact with LYS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B GLU* 2.9 19.4 + - + +
359B THR* 1.3 87.7 - - - +
361B ASN* 1.4 60.3 + - - +
362B GLN 3.4 16.7 - - - +
363B VAL* 4.7 0.2 - - - +
414B LYS* 2.8 31.0 + - - +
347G GLN* 3.6 38.0 - - - +
349G TYR* 4.1 13.0 - - - +
370G LYS* 5.5 3.4 - - - +
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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