Contacts of the helix formed by residues 348 - 361 (chain A) in PDB entry 3V3K
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 TRP 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A TRP* 3.4 29.6 + + + +
341A ARG* 4.6 1.3 - - - +
342A ASP* 4.8 6.2 - - + +
346A GLY 4.4 7.0 - - - -
347A SER* 1.3 74.4 + - - +
349A TYR* 1.3 61.4 + - - +
351A GLU* 4.1 4.2 - - - +
352A THR* 2.7 32.9 + - - -
377A VAL* 3.7 11.1 - - + +
380A LYS* 3.6 62.1 - - + +
381A GLY* 3.9 11.9 - - - -
383A TYR 3.4 22.2 - - - -
385A GLN* 3.2 39.3 - - + +
186B LEU* 3.4 40.4 - - + +
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Residues in contact with TYR 349 (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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281A PHE* 3.5 21.9 - - + -
282A ILE 4.8 0.9 - - - -
283A GLN* 3.4 31.0 - - + +
330A SER* 2.6 37.7 + - - -
331A TYR 4.0 3.4 - - - -
332A SER* 3.6 37.5 - - - +
347A SER* 3.3 1.4 + - - -
348A TRP* 1.3 80.2 - - - +
350A VAL* 1.3 63.9 + - + +
352A THR* 3.7 1.9 - - - -
353A LEU* 2.8 54.5 + - + +
370A LEU* 4.4 3.6 - - + +
373A VAL* 4.0 22.2 - - + +
377A VAL* 4.3 7.6 - - - +
385A GLN* 4.4 7.9 + - - +
387A PRO* 4.1 11.4 - - + -
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASP* 3.5 54.7 - - + +
188A LYS* 4.9 6.1 - - + -
189A LEU* 3.8 21.3 - - + -
235A LEU* 4.3 9.2 - - + -
283A GLN* 4.2 14.6 - - + -
347A SER* 3.5 11.2 + - - -
349A TYR* 1.3 88.9 - - + +
351A GLU* 1.3 59.9 + - - +
353A LEU* 3.6 6.9 - - + +
354A ASP* 2.9 29.7 + - + +
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Residues in contact with GLU 351 (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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185A ASP* 4.2 4.1 + - - +
188A LYS* 3.7 28.7 + - - +
345A SER* 3.8 27.0 - - - +
346A GLY 4.4 4.2 - - - +
347A SER 2.9 20.4 + - - +
348A TRP* 4.1 5.6 - - - +
350A VAL* 1.3 75.4 - - - +
352A THR* 1.3 61.5 + - - +
354A ASP* 4.2 1.9 - - - +
355A ASP* 3.3 24.5 + - + +
380A LYS* 3.9 19.1 + - - +
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Residues in contact with THR 352 (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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348A TRP 2.7 22.3 + - - -
349A TYR 3.8 1.1 - - - -
351A GLU* 1.3 73.9 - - - +
353A LEU* 1.3 64.7 + - - +
355A ASP* 4.0 4.4 - - + +
356A ILE* 3.1 37.5 + - + +
373A VAL* 3.8 10.5 - - - -
376A ALA* 3.3 32.7 - - + +
377A VAL* 3.5 15.5 - - + +
380A LYS* 3.9 18.2 + - - -
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.9 25.8 - - + -
192A ARG* 5.4 1.6 - - + -
193A PHE* 5.4 3.8 - - + -
281A PHE* 4.2 20.2 - - + -
349A TYR* 2.8 57.2 + - + +
350A VAL* 3.2 8.7 + - + +
352A THR* 1.3 75.5 - - - +
354A ASP* 1.3 60.2 + - - +
356A ILE* 3.8 0.5 - - - +
357A PHE* 2.8 68.7 + - + -
370A LEU* 4.6 3.8 - - + -
373A VAL* 3.9 14.8 - - + +
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Residues in contact with ASP 354 (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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188A LYS* 3.7 42.8 - - + +
189A LEU* 5.4 2.7 - - + -
191A ARG* 4.9 5.9 + - - -
192A ARG* 2.9 45.4 + - - +
350A VAL* 2.9 17.5 + - + +
351A GLU 4.2 2.5 - - - +
353A LEU* 1.3 80.8 - - + +
355A ASP* 1.3 58.6 + - - +
357A PHE* 3.8 4.7 - - - +
358A GLU* 3.0 28.4 + - - +
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Residues in contact with ASP 355 (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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351A GLU* 3.3 18.2 + - + +
352A THR* 4.0 6.7 - - - +
353A LEU 3.3 0.2 - - - -
354A ASP* 1.3 80.2 - - - +
356A ILE* 1.3 64.8 + - + +
358A GLU* 3.4 8.2 + - - +
359A GLN* 2.8 51.1 + - - +
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Residues in contact with ILE 356 (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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352A THR* 3.1 29.9 + - + +
353A LEU 4.0 2.2 - - - +
355A ASP* 1.3 76.7 - - + +
357A PHE* 1.3 61.2 + - + +
358A GLU 3.2 0.4 - - - -
359A GLN* 3.3 2.0 + - - +
360A TRP* 2.9 37.8 + - + +
369A LEU* 3.6 30.8 - - + +
372A ARG* 3.3 35.2 - - + +
373A VAL* 3.2 36.3 - - + +
376A ALA* 4.3 3.1 - - + -
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Residues in contact with PHE 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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192A ARG* 3.8 27.6 + - + -
193A PHE* 4.6 8.3 - + - -
196A LEU* 4.1 19.5 - - + -
281A PHE* 4.7 6.5 - + - -
353A LEU* 2.8 51.5 + - + +
354A ASP 3.8 4.5 - - - +
356A ILE* 1.3 75.8 - - + +
358A GLU* 1.3 62.7 + - - +
361A ALA* 2.9 32.4 - - + +
366A LEU* 4.0 12.6 - - + -
369A LEU* 3.9 30.1 - - + -
370A LEU* 4.5 8.5 - - + -
373A VAL* 5.3 0.7 - - + -
400A PHE* 3.6 37.5 - + - -
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Residues in contact with GLU 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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192A ARG* 2.8 36.9 + - - +
354A ASP 3.0 14.8 + - - +
355A ASP* 3.4 12.1 - - - +
357A PHE* 1.3 78.4 - - - +
359A GLN* 1.3 69.8 + - + +
361A ALA* 4.4 2.8 + - - +
362A HIS* 4.6 6.8 + - - -
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Residues in contact with GLN 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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355A ASP* 2.8 38.3 + - - +
356A ILE* 3.3 2.3 + - - -
358A GLU* 1.3 87.8 - - + +
360A TRP* 1.3 93.7 + - + +
361A ALA 3.8 0.2 - - - -
362A HIS* 3.2 24.0 + - - -
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Residues in contact with TRP 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 2.9 18.9 + - + -
359A GLN* 1.3 106.4 + - + +
361A ALA* 1.3 63.5 + - - +
362A HIS* 3.4 5.2 - - - +
363A SER* 3.7 18.8 - - - -
364A GLU* 3.2 49.1 + - - +
369A LEU* 3.2 24.7 - - + +
372A ARG* 3.6 44.0 - - - +
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Residues in contact with ALA 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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146A ARG* 4.4 1.6 + - - -
192A ARG* 5.8 0.2 - - - +
196A LEU* 4.5 20.6 - - + -
357A PHE* 2.9 31.1 + - + +
358A GLU 4.4 2.1 + - - +
359A GLN 3.8 0.8 - - - -
360A TRP* 1.3 77.5 - - - +
362A HIS* 1.3 64.2 + - - +
364A GLU 3.4 13.2 - - - +
369A LEU* 3.9 14.9 - - + +
399A PHE* 5.6 0.2 - - - -
400A PHE* 4.2 19.3 + - + +
402A THR* 4.9 7.2 - - + -
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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