Contacts of the helix formed by residues 360 - 366 (chain A) in PDB entry 3W3K
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 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A GLU 4.9 0.2 - - - -
327A ILE 3.1 18.9 + - - -
328A ALA 3.1 25.1 + - - -
329A SER 2.8 23.9 + - - -
330A GLY* 5.0 1.1 - - - -
333A LEU* 5.6 0.9 - - - -
358A ASN* 3.9 0.4 + - - -
359A ILE* 1.3 74.2 - - - +
361A ARG* 1.3 58.7 + - - +
362A ASN* 2.9 21.7 + - - +
363A PHE* 3.0 34.6 + - - +
389A PRO* 3.6 2.3 - - - +
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Residues in contact with ARG 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ILE 3.5 2.0 + - - +
360A SER* 1.3 71.1 + - - +
362A ASN* 1.3 52.7 + - - +
363A PHE 3.1 0.9 - - - -
364A SER* 2.6 38.3 + - - -
365A LYS* 4.7 1.4 + - - +
388A GLN* 4.6 19.5 + - - +
389A PRO* 3.5 19.6 - - + +
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Residues in contact with ASN 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A SER 3.5 17.4 + - - -
330A GLY 4.0 17.6 + - - +
331A ALA* 4.7 5.9 - - - +
333A LEU* 3.6 16.5 - - + +
334A THR* 4.4 14.8 + - - +
360A SER* 2.9 10.5 + - - +
361A ARG* 1.3 75.4 - - - +
363A PHE* 1.3 54.9 - - - +
364A SER 3.0 5.8 - - - +
365A LYS* 3.0 42.6 + - + +
366A LEU 4.2 0.5 + - - -
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Residues in contact with PHE 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ILE* 3.5 26.0 - - + -
333A LEU* 3.3 31.9 - - + -
342A LEU* 3.9 17.7 - - + -
344A LEU* 3.6 25.6 - - + -
359A ILE* 3.5 28.7 - - + -
360A SER* 3.0 27.6 + - - +
362A ASN* 1.3 75.2 - - - +
364A SER* 1.3 59.9 + - - +
365A LYS 3.0 3.7 + - - -
366A LEU* 3.3 23.9 + - + +
369A LEU* 5.2 0.4 - - + -
372A LEU* 4.1 14.8 - - + -
374A LEU* 5.6 0.4 - - + -
389A PRO* 3.7 6.3 - - + -
390A LEU* 3.8 27.4 - - + -
393A LEU* 3.6 15.9 - - - +
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A ARG 2.6 20.9 + - - -
363A PHE* 1.3 79.2 - - - +
365A LYS* 1.3 79.5 + - - +
366A LEU 3.3 0.8 + - - -
367A LEU* 3.7 11.4 - - - +
389A PRO* 3.3 22.8 + - - -
392A GLN* 6.0 5.2 - - - -
393A LEU* 3.6 15.3 - - - +
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Residues in contact with LYS 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A LEU 3.7 16.4 - - - +
334A THR* 4.3 23.5 - - + +
337A PRO* 4.1 12.8 - - - +
361A ARG 4.9 1.2 + - - -
362A ASN* 3.0 32.5 + - - +
364A SER* 1.3 94.4 + - - +
366A LEU* 1.3 59.7 - - - +
367A LEU* 3.2 15.4 + - - +
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A LEU* 3.7 32.5 - - + +
336A LEU* 3.5 34.1 - - + +
339A LEU* 4.5 11.4 - - + +
342A LEU* 3.8 20.4 - - + -
362A ASN 4.7 0.2 - - - +
363A PHE* 3.3 26.4 + - + +
364A SER 3.3 1.6 - - - -
365A LYS* 1.3 77.0 - - - +
367A LEU* 1.3 61.0 + - - +
368A SER 3.4 2.6 + - - -
369A LEU* 3.7 38.9 + - + +
393A LEU* 3.1 24.8 - - - +
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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