Contacts of the helix formed by residues 348 - 361 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340G TRP* 3.5 34.3 + + + +
342G ASP* 4.6 14.4 - - + +
345G SER* 5.3 0.9 - - - -
346G GLY 4.4 7.4 - - - -
347G SER* 1.3 72.9 + - - +
349G TYR* 1.3 59.9 + - - +
351G GLU* 4.9 2.9 - - - -
352G THR* 2.7 32.4 + - - -
377G VAL* 3.6 14.2 - - + +
380G LYS* 3.5 57.4 + - + +
381G GLY* 3.9 12.8 - - - -
383G TYR 3.2 28.3 - - - -
384G LYS* 4.7 3.8 - - - -
385G GLN* 4.1 21.8 - - + +
186H LEU* 3.5 32.5 - - + +
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Residues in contact with TYR 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281G PHE* 3.5 11.5 - - + -
282G ILE 4.7 10.8 - - - -
283G GLN* 3.5 21.3 - - + +
330G SER* 2.7 38.9 + - - -
331G TYR 4.3 2.5 - - - -
332G SER* 3.5 38.1 - - - -
347G SER* 3.3 1.2 + - - -
348G TRP* 1.3 80.0 - - - +
350G VAL* 1.3 64.3 + - + +
352G THR* 3.3 3.6 + - - -
353G LEU* 2.8 65.5 + - + +
370G LEU* 3.9 3.3 - - + +
373G VAL* 4.1 19.3 - - + +
377G VAL* 4.1 7.8 - - + +
385G GLN* 4.3 8.1 - - - +
387G PRO* 4.2 10.5 - - + -
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Residues in contact with VAL 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G ASP* 3.5 39.9 - - + +
188G LYS* 5.0 5.2 - - + -
189G LEU* 3.8 32.3 - - + -
235G LEU* 4.2 7.4 - - + -
283G GLN* 4.1 15.3 - - + -
347G SER* 3.4 15.2 + - - +
349G TYR* 1.3 90.1 - - + +
351G GLU* 1.3 60.7 + - - +
353G LEU* 4.1 5.8 - - + -
354G ASP* 3.0 30.1 + - - +
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Residues in contact with GLU 351 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G ASP* 4.3 2.2 + - - +
188G LYS* 3.6 28.0 + - - +
345G SER* 3.2 39.1 + - - +
346G GLY 4.7 0.5 - - - +
347G SER 2.9 18.3 + - - +
348G TRP* 4.2 5.0 - - - +
350G VAL* 1.3 76.5 - - - +
352G THR* 1.3 62.5 + - - +
354G ASP* 3.8 1.9 + - - +
355G ASP* 3.2 24.2 + - + +
380G LYS* 3.2 25.2 + - - +
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Residues in contact with THR 352 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348G TRP 2.7 22.9 + - - -
349G TYR 3.7 2.7 - - - -
351G GLU* 1.3 75.3 - - - +
353G LEU* 1.3 64.0 + - - +
355G ASP* 3.8 4.6 - - + +
356G ILE* 3.1 36.7 + - + +
373G VAL* 3.8 13.0 - - - +
376G ALA* 3.3 33.9 - - + +
377G VAL* 3.6 9.5 - - + +
380G LYS* 3.7 18.0 + - - -
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Residues in contact with LEU 353 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G LEU* 4.0 23.6 - - + -
192G ARG* 5.6 1.1 - - + -
193G PHE* 5.4 3.4 - - + -
281G PHE* 3.8 21.1 - - + -
349G TYR* 2.8 59.7 + - + +
350G VAL* 3.3 8.5 + - + +
352G THR* 1.3 73.2 - - - +
354G ASP* 1.3 60.6 + - - +
356G ILE* 3.4 1.4 + - - -
357G PHE* 3.0 68.6 + - + -
370G LEU* 4.4 4.0 - - + -
373G VAL* 3.9 14.1 - - + -
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Residues in contact with ASP 354 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G LYS* 3.5 43.3 - - + +
189G LEU* 5.1 5.6 - - + -
192G ARG* 2.8 49.0 + - - +
350G VAL 3.0 17.5 + - - +
351G GLU 4.1 2.9 - - - +
353G LEU* 1.3 81.1 - - - +
355G ASP* 1.3 62.6 + - - +
357G PHE* 4.5 2.9 - - - -
358G GLU* 3.1 23.2 + - - +
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Residues in contact with ASP 355 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351G GLU* 3.2 18.6 + - + +
352G THR* 3.8 7.8 - - + +
353G LEU 3.3 0.2 - - - -
354G ASP* 1.3 79.4 - - - +
356G ILE* 1.3 63.9 + - - +
358G GLU* 3.5 7.8 + - - +
359G GLN* 3.2 37.4 + - - +
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Residues in contact with ILE 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352G THR* 3.1 21.3 + - + +
353G LEU 4.0 2.2 - - - +
355G ASP* 1.3 80.3 - - - +
357G PHE* 1.3 57.0 + - - +
359G GLN* 4.6 1.6 - - - +
360G TRP* 2.7 43.9 + - + +
369G LEU* 3.6 32.3 - - + +
372G ARG* 3.4 30.1 - - + +
373G VAL* 3.2 44.4 - - + +
376G ALA* 4.4 3.6 - - + -
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Residues in contact with PHE 357 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G ARG* 3.8 26.2 + - + -
193G PHE* 4.8 9.2 - + - -
196G LEU* 4.0 21.2 - - + +
281G PHE* 4.6 8.3 - + - -
353G LEU* 3.0 51.3 + - + +
354G ASP 4.0 1.1 - - - +
356G ILE* 1.3 76.8 - - + +
358G GLU* 1.3 64.0 + - - +
361G ALA* 2.9 34.5 + - + +
362G HIS 4.9 0.2 + - - -
366G LEU* 4.2 12.3 - - + -
369G LEU* 3.8 34.5 - - + -
370G LEU* 5.0 6.5 - - + -
373G VAL* 5.2 1.1 - - + -
400G PHE* 3.6 29.8 - + - -
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Residues in contact with GLU 358 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G ARG* 3.3 35.7 + - - +
354G ASP 3.1 18.8 + - - +
355G ASP* 3.6 8.1 - - - +
356G ILE 3.3 0.2 - - - -
357G PHE* 1.3 79.1 - - - +
359G GLN* 1.3 63.6 + - + +
362G HIS* 4.6 6.9 + - - -
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Residues in contact with GLN 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355G ASP* 3.2 26.4 + - - +
356G ILE* 5.4 1.2 - - - +
358G GLU* 1.3 84.0 - - + +
360G TRP* 1.3 99.3 + - + +
362G HIS* 3.3 19.7 - - - -
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Residues in contact with TRP 360 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356G ILE* 2.7 27.9 + - + +
359G GLN* 1.3 116.8 + - + +
361G ALA* 1.3 58.4 + - - +
362G HIS* 3.2 6.5 + + - -
363G SER* 3.3 17.5 + - - -
364G GLU* 3.0 53.6 + - - +
369G LEU* 3.6 12.6 - - + -
372G ARG* 3.1 44.7 - - - +
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Residues in contact with ALA 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G LEU* 4.7 8.5 - - + -
357G PHE* 2.9 40.8 + - + +
358G GLU 4.8 0.2 + - - -
359G GLN 4.0 0.4 - - - -
360G TRP* 1.3 76.4 - - - +
362G HIS* 1.3 61.7 + - - +
363G SER 3.4 0.2 - - - -
364G GLU 3.4 11.9 - - - +
369G LEU* 3.6 22.3 - - + +
399G PHE* 5.5 1.0 - - - -
400G PHE* 4.2 20.5 + - + +
402G THR* 4.3 12.0 - - + +
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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