Contacts of the helix formed by residues 356 - 362 (chain A) in PDB entry 1V8K
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 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A GLU* 4.9 3.1 - - - -
332A LYS* 4.0 17.5 - - - -
333A SER* 3.3 38.0 - - - -
336A ALA* 3.8 3.0 - - - +
355A GLU* 1.3 80.0 + - - +
357A LYS* 1.3 66.9 + - - +
358A LEU 3.8 0.3 + - - -
359A THR* 3.2 18.7 + - - +
360A GLN* 3.0 24.9 + - - +
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Residues in contact with LYS 357 (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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218A ILE* 3.7 23.1 - - + -
221A GLY* 3.3 40.1 + - - +
222A LYS* 5.4 0.2 - - - +
223A VAL* 4.3 13.2 - - + -
235A VAL* 3.7 34.0 + - - +
329A GLU* 5.2 3.5 + - + -
356A SER* 1.3 75.2 - - - +
358A LEU* 1.3 65.2 + - - +
360A GLN* 2.9 29.7 + - - +
361A VAL* 2.9 27.3 + - + +
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Residues in contact with LEU 358 (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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159A PHE* 5.2 0.9 - - + -
216A PHE* 6.2 0.2 - - + -
218A ILE* 3.5 22.0 - - + +
285A HIS* 3.9 31.0 - - + +
287A CYS* 5.8 4.3 - - + -
305A VAL* 4.3 17.3 - - + -
307A LEU* 3.7 23.3 - - + -
333A SER* 4.3 18.2 - - - +
334A LEU* 5.5 0.7 - - + -
337A LEU* 4.6 17.0 - - + -
356A SER* 3.4 7.5 + - - +
357A LYS* 1.3 79.7 - - - +
359A THR* 1.3 58.6 + - + +
361A VAL* 3.4 1.6 + - - +
362A LEU* 3.1 54.5 + - + +
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Residues in contact with THR 359 (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 SER 4.2 2.0 - - - +
336A ALA* 3.6 15.5 - - + +
337A LEU* 3.5 43.1 - - + +
340A CYS* 3.7 21.0 - - + -
355A GLU* 2.9 24.5 + - - +
356A SER* 3.2 18.0 + - - +
357A LYS 3.3 0.2 - - - -
358A LEU* 1.3 76.3 - - + +
360A GLN* 1.3 59.6 + - - +
362A LEU* 3.9 5.8 - - - +
363A ARG* 3.1 26.3 + - - +
366A PHE* 4.8 2.6 - - + -
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Residues in contact with GLN 360 (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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235A VAL* 3.4 15.9 + - + +
236A LEU 5.4 0.2 - - - -
237A GLU* 3.2 26.1 + - - +
243A VAL* 3.2 37.8 - - + +
355A GLU* 3.7 5.6 - - + +
356A SER 3.0 17.3 + - - +
357A LYS* 2.9 42.8 + - - +
359A THR* 1.3 79.6 - - - +
361A VAL* 1.3 63.2 + - - +
363A ARG* 3.2 30.9 - - - +
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Residues in contact with VAL 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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216A PHE* 3.7 31.6 - - + -
218A ILE* 4.4 6.5 - - + -
223A VAL* 4.3 22.2 - - + -
235A VAL* 4.4 12.3 - - + -
243A VAL* 4.2 8.9 - - - +
245A VAL* 4.1 27.1 - - + +
289A GLN* 5.6 2.3 - - - +
301A LYS* 5.5 1.9 + - - -
357A LYS* 2.9 20.1 + - + +
358A LEU 3.8 3.8 - - - +
360A GLN* 1.3 78.5 - - + +
362A LEU* 1.3 64.2 + - + +
363A ARG 3.3 0.4 - - - -
364A ASP* 3.6 13.0 - - - +
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Residues in contact with LEU 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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157A THR* 5.0 3.8 - - + -
159A PHE* 3.8 32.5 - - + -
216A PHE* 5.0 0.7 - - + -
287A CYS* 4.2 12.3 - - - -
289A GLN* 4.5 5.8 - - - +
301A LYS* 6.5 0.2 - - - -
303A SER* 3.8 29.6 - - - +
305A VAL* 3.9 8.7 - - + -
337A LEU* 5.5 0.4 - - + -
358A LEU* 3.1 36.4 + - + +
359A THR* 3.9 1.8 - - - -
361A VAL* 1.3 84.7 - - + +
363A ARG* 1.3 63.9 + - - +
364A ASP* 3.3 3.8 - - - -
365A SER* 2.9 22.1 + - - +
366A PHE* 3.2 25.4 - - + -
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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