Contacts of the helix formed by residues 348 - 361 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340C TRP* 3.5 39.9 + + + +
342C ASP* 4.6 16.5 - - + +
346C GLY 4.6 1.3 - - - -
347C SER* 1.3 75.2 + - - +
349C TYR* 1.3 60.2 - - - +
351C GLU* 4.3 1.7 - - - +
352C THR* 2.7 32.7 + - - -
377C VAL* 3.7 11.5 - - + +
380C LYS* 3.5 59.3 - - + +
381C GLY* 3.8 9.9 - - - -
382C ILE 5.1 0.2 - - - -
383C TYR 3.3 27.1 - - - -
384C LYS* 4.6 3.6 - - - -
385C GLN* 4.2 23.1 - - + +
186D LEU* 3.4 39.7 - - + +
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Residues in contact with TYR 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C VAL* 6.6 0.2 - - + -
281C PHE* 3.5 11.9 - - + -
282C ILE 4.7 3.8 - - - -
283C GLN* 3.5 30.5 - - + +
330C SER* 2.6 38.8 + - - -
331C TYR 3.9 15.7 - - - -
332C SER* 3.7 26.5 - - - -
347C SER* 3.3 1.4 + - - -
348C TRP* 1.3 79.2 - - - +
350C VAL* 1.3 64.2 + - + +
352C THR* 3.3 4.2 + - - -
353C LEU* 2.8 62.3 + - + +
370C LEU* 3.9 2.9 - - + +
373C VAL* 4.1 22.4 - - + +
377C VAL* 4.3 6.7 - - - -
385C GLN* 4.1 8.2 - - - +
387C PRO* 4.2 7.6 - - + -
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Residues in contact with VAL 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ASP* 3.5 44.9 - - + +
188C LYS* 4.9 6.1 - - + -
189C LEU* 3.7 32.3 - - + -
235C LEU* 4.0 21.1 - - + -
283C GLN* 4.2 8.3 - - + -
347C SER* 3.8 3.1 + - - -
349C TYR* 1.3 88.5 - - + +
351C GLU* 1.3 60.6 + - - +
353C LEU* 3.5 6.9 - - + +
354C ASP* 2.8 30.3 + - - +
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Residues in contact with GLU 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ASP* 4.4 2.1 + - - +
188C LYS* 3.5 28.6 + - - +
345C SER* 3.0 39.3 + - - +
346C GLY 4.4 1.0 - - - +
347C SER 3.1 18.8 + - - +
348C TRP* 4.3 3.8 - - - +
350C VAL* 1.3 78.9 - - - +
352C THR* 1.3 60.9 + - - +
354C ASP* 3.6 1.9 + - - +
355C ASP* 3.2 24.1 + - + +
380C LYS* 3.5 22.0 + - - +
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Residues in contact with THR 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C TRP 2.7 22.5 + - - -
349C TYR 3.3 2.3 + - - -
351C GLU* 1.3 74.6 - - - +
353C LEU* 1.3 64.8 + - - +
355C ASP* 4.1 4.8 - - + +
356C ILE* 3.3 36.6 + - + +
373C VAL* 3.9 5.6 - - - -
376C ALA* 3.4 32.5 - - + -
377C VAL* 3.5 19.8 - - + +
380C LYS* 4.0 17.3 + - - -
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Residues in contact with LEU 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C LEU* 4.3 22.2 - - + -
192C ARG* 5.7 1.1 - - + -
193C PHE* 5.3 3.1 - - + -
281C PHE* 3.7 21.3 - - + -
349C TYR* 2.8 54.6 + - + +
350C VAL* 3.5 9.2 - - + +
352C THR* 1.3 77.7 - - - +
354C ASP* 1.3 58.6 + - - +
356C ILE 4.0 0.2 - - - -
357C PHE* 3.0 71.8 + - + -
370C LEU* 4.4 7.4 - - + -
373C VAL* 4.0 9.8 - - + +
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Residues in contact with ASP 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LYS* 3.3 47.2 - - + +
189C LEU* 5.2 5.1 - - + +
192C ARG* 2.7 47.9 + - - +
350C VAL 2.8 19.1 + - - +
351C GLU 4.0 3.1 - - - +
353C LEU* 1.3 76.8 - - - +
355C ASP* 1.3 57.6 + - - +
357C PHE* 4.0 3.7 - - - -
358C GLU* 3.1 26.7 + - - +
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Residues in contact with ASP 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C GLU* 3.2 17.9 + - + +
352C THR* 4.1 7.0 - - - +
353C LEU 3.3 0.2 - - - -
354C ASP* 1.3 76.8 - - - +
356C ILE* 1.3 62.3 + - + +
358C GLU* 3.4 8.4 + - - +
359C GLN* 3.1 36.9 + - - +
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Residues in contact with ILE 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C THR* 3.3 21.3 + - + +
353C LEU 4.1 2.5 - - - +
355C ASP* 1.3 78.5 - - + +
357C PHE* 1.3 58.4 + - + +
359C GLN* 4.7 1.1 - - - +
360C TRP* 2.7 43.3 + - + +
361C ALA 3.7 0.5 + - - -
369C LEU* 3.7 35.1 - - + +
372C ARG* 3.3 27.8 - - + +
373C VAL* 3.2 45.1 - - + +
376C ALA* 4.6 2.0 - - + -
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Residues in contact with PHE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ARG* 3.9 27.1 + - + -
193C PHE* 4.7 9.6 - + - -
196C LEU* 3.9 22.2 - - + +
281C PHE* 4.6 7.2 - + - -
353C LEU* 3.0 53.2 + - + +
354C ASP 4.1 1.1 - - - +
356C ILE* 1.3 75.3 - - + +
358C GLU* 1.3 65.1 + - - +
361C ALA* 2.9 29.3 + - + +
366C LEU* 4.1 19.7 - - + -
369C LEU* 3.7 37.7 - - + -
370C LEU* 4.9 7.2 - - + -
373C VAL* 5.3 1.1 - - + -
400C PHE* 3.8 23.8 - + - -
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Residues in contact with GLU 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ARG* 3.1 36.5 + - - +
354C ASP 3.1 18.8 + - - +
355C ASP* 3.5 10.5 - - - +
356C ILE 3.3 0.2 - - - -
357C PHE* 1.3 79.1 - - - +
359C GLN* 1.3 63.9 + - + +
362C HIS* 4.8 6.4 + - - -
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Residues in contact with GLN 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C ASP* 3.1 24.9 + - - +
356C ILE* 5.5 0.9 - - - +
358C GLU* 1.3 82.0 - - + +
360C TRP* 1.3 103.0 + - + +
361C ALA 3.9 0.2 - - - -
362C HIS* 3.3 23.7 - - - -
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Residues in contact with TRP 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C ILE* 2.7 27.8 + - + +
359C GLN* 1.3 121.1 + - + +
361C ALA* 1.3 58.6 + - - +
362C HIS* 3.3 4.7 - + - -
363C SER* 3.3 16.9 + - - -
364C GLU* 3.0 55.0 + - - +
369C LEU* 3.5 14.4 - - + -
372C ARG* 3.1 40.6 - - - +
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Residues in contact with ALA 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C LEU* 4.6 11.2 - - + -
356C ILE 3.7 2.4 + - - -
357C PHE* 2.9 37.3 + - + +
358C GLU 4.8 0.2 + - - -
359C GLN 3.9 0.6 - - - -
360C TRP* 1.3 77.2 - - - +
362C HIS* 1.3 61.2 + - - +
364C GLU 3.4 12.0 - - - +
369C LEU* 3.9 20.1 - - + +
399C PHE* 5.7 1.4 - - - -
400C PHE* 4.3 16.0 + - + +
402C THR* 3.9 16.4 - - + +
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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