Contacts of the helix formed by residues 313 - 333 (chain D) in PDB entry 3GV5
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 313 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D CYS* 3.7 3.5 - - - -
312D SER* 1.3 82.6 - - - +
314D GLU* 1.4 63.2 + - - +
315D VAL* 3.9 9.7 - - - +
316D GLU* 2.9 31.4 + - - +
317D ALA* 2.8 23.0 + - - +
401D PHE* 3.5 11.2 - - - -
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Residues in contact with GLU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D SER* 1.4 75.7 - - - +
315D VAL* 1.4 70.5 + - - +
316D GLU 3.2 0.5 + - - -
317D ALA* 3.4 11.0 - - - +
318D LYS* 3.1 25.1 - - - +
388D MSE 3.5 20.2 - - + +
391D PHE* 3.8 24.0 - - + -
392D ARG* 3.8 26.8 + - - -
397D VAL* 4.4 22.6 - - + +
401D PHE* 4.6 5.6 - - + -
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Residues in contact with VAL 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D SER* 3.9 13.2 - - - +
314D GLU* 1.4 74.6 + - - +
316D GLU* 1.3 68.1 + - + +
318D LYS* 3.2 7.4 + - - +
319D ASN* 3.1 43.8 + - - +
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Residues in contact with GLU 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D LYS 4.8 5.3 - - - +
311D CYS* 3.7 15.3 - - - -
312D SER* 3.2 29.1 + - - -
313D SER* 2.9 32.1 + - - +
315D VAL* 1.3 77.8 - - + +
317D ALA* 1.4 70.5 + - - +
318D LYS 2.8 3.9 + - - -
319D ASN* 3.4 6.6 + - - +
320D LYS* 3.1 19.2 + - - +
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D CYS* 3.6 10.6 - - - -
313D SER 2.8 11.1 + - - +
314D GLU* 3.4 12.8 - - - +
316D GLU* 1.4 77.6 - - - +
318D LYS* 1.3 55.3 + - - +
320D LYS* 3.2 4.3 + - - +
321D ILE* 2.8 37.8 + - + +
388D MSE 3.9 10.1 - - + -
391D PHE* 3.7 36.3 - - + -
406D LEU* 4.0 6.6 - - + +
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Residues in contact with LYS 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D GLU* 3.1 24.0 - - - +
315D VAL* 3.4 7.6 - - - +
316D GLU 2.8 3.0 + - - -
317D ALA* 1.3 74.7 - - - +
319D ASN* 1.3 59.5 + - - +
321D ILE* 3.3 3.2 + - - +
322D GLU* 2.8 54.0 + - - +
384D VAL* 3.6 24.2 - - + -
385D ASP* 5.4 4.6 + - - -
388D MSE 3.8 31.4 - - + -
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Residues in contact with ASN 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D VAL* 3.2 33.5 + - - +
316D GLU* 3.9 6.4 - - - +
318D LYS* 1.3 83.2 - - - +
320D LYS* 1.3 63.7 + - - +
322D GLU* 3.5 19.3 + - - +
323D GLU* 3.2 22.6 + - - +
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Residues in contact with LYS 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D ASP* 2.7 37.8 + - + +
308D PHE* 4.2 25.1 - - + -
316D GLU 3.1 13.2 + - - +
317D ALA 3.6 7.9 - - - +
319D ASN* 1.3 74.3 - - - +
321D ILE* 1.3 64.9 + - - +
323D GLU* 3.2 37.6 + - - +
324D LEU* 3.0 33.9 + - + +
406D LEU* 4.3 12.3 - - + -
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Residues in contact with ILE 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ALA* 2.8 33.3 + - + +
318D LYS* 3.3 6.0 + - - +
320D LYS* 1.3 71.8 - - - +
322D GLU* 1.3 58.1 + - - +
324D LEU* 3.3 7.4 + - - +
325D LEU* 2.8 29.2 + - + +
344D LEU* 4.2 26.0 - - + -
384D VAL* 5.5 6.5 - - + -
387D LEU* 3.7 36.1 - - + +
388D MSE 3.6 26.2 - - - -
391D PHE* 4.3 11.2 - - + -
406D LEU* 4.3 14.6 - - + -
408D VAL* 4.1 8.9 - - + +
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Residues in contact with GLU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D LYS* 2.8 52.8 + - - +
319D ASN* 3.7 19.7 - - - +
321D ILE* 1.3 74.0 - - - +
323D GLU* 1.3 55.8 + - - +
325D LEU* 3.5 3.3 + - - +
326D ALA* 3.0 24.4 + - - +
380D MSE 3.1 27.8 - - + +
384D VAL* 3.8 27.1 - - + +
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Residues in contact with GLU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D ASP* 4.7 2.1 - - - +
319D ASN 3.2 11.4 + - - +
320D LYS* 3.2 43.6 + - - +
322D GLU* 1.3 76.0 - - - +
324D LEU* 1.3 69.3 + - + +
326D ALA* 3.4 7.2 + - - +
327D SER* 3.4 23.0 + - - +
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Residues in contact with LEU 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D GLU* 3.7 42.5 - - + +
305D GLU 3.8 15.0 - - - +
306D ASP* 4.1 7.9 - - + +
320D LYS* 3.0 26.8 + - + +
321D ILE* 3.6 9.0 - - + +
323D GLU* 1.3 79.5 - - + +
325D LEU* 1.3 62.6 + - - +
327D SER* 3.3 8.2 + - - -
328D LEU* 3.2 19.3 + - - +
406D LEU* 3.5 38.6 - - + +
407D SER* 3.9 4.0 - - - -
408D VAL* 4.1 17.3 - - + -
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Residues in contact with LEU 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D ILE* 2.8 17.3 + - + +
322D GLU 3.8 3.1 - - - +
324D LEU* 1.3 77.6 - - - +
326D ALA* 1.3 55.7 + - - +
328D LEU* 3.0 8.6 + - - +
329D LEU* 2.9 45.1 + - + +
380D MSE 3.7 20.9 - - - +
383D MSE 3.6 29.2 - - + -
384D VAL* 3.8 20.2 - - + +
387D LEU* 4.0 22.2 - - + -
408D VAL* 4.6 7.3 - - + +
410D PHE* 3.7 31.2 - - + -
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Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D GLU 3.0 17.6 + - - +
323D GLU* 3.7 7.6 - - - +
324D LEU 3.3 0.2 - - - -
325D LEU* 1.3 76.8 - - - +
327D SER* 1.3 61.8 + - - +
329D LEU* 3.4 11.9 + - - +
330D ASN* 3.5 19.7 + - - +
380D MSE 3.8 19.0 - - + +
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Residues in contact with SER 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D GLU* 3.6 27.6 + - - -
323D GLU* 3.4 8.9 + - - +
324D LEU* 3.3 10.7 + - - -
326D ALA* 1.3 78.1 - - - +
328D LEU* 1.3 55.9 + - - +
330D ASN* 2.7 29.4 - - - +
331D ARG* 3.5 12.4 - - - +
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D PHE* 3.6 37.9 - - + +
303D SER 3.8 2.2 - - - -
304D GLU* 3.7 22.7 - - + -
324D LEU 3.2 6.0 + - - +
325D LEU* 3.0 11.0 + - - +
327D SER* 1.3 78.4 - - - +
329D LEU* 1.3 54.5 + - - +
331D ARG* 2.7 29.5 + - - +
332D VAL* 3.1 16.5 + - - +
408D VAL* 3.4 48.9 - - + +
409D CYS 4.2 1.6 - - - +
410D PHE* 3.8 28.0 - - + +
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Residues in contact with LEU 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D LEU* 2.9 40.9 + - + +
326D ALA* 3.4 5.1 + - - +
327D SER 3.3 1.0 - - - -
328D LEU* 1.3 74.6 - - - +
330D ASN* 1.3 62.7 + - - +
331D ARG 3.1 0.5 + - - -
332D VAL* 3.7 6.0 - - + +
333D CYS* 3.1 27.6 + - - +
371D LYS* 4.3 22.0 - - + -
379D VAL* 4.7 16.2 - - + +
380D MSE 3.9 25.8 - - + -
383D MSE 4.8 2.0 - - + -
410D PHE* 3.6 27.8 - - + -
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Residues in contact with ASN 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D ALA 3.5 17.4 + - - +
327D SER* 2.7 29.5 + - - +
329D LEU* 1.3 67.8 + - - +
331D ARG* 1.3 64.0 + - + +
333D CYS* 3.3 19.6 + - - +
334D GLN* 3.5 18.5 + - - +
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Residues in contact with ARG 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D THR* 6.0 1.6 - - - -
103D ARG* 3.2 46.7 - - - +
302D PHE* 3.8 40.5 - - + +
303D SER 2.8 25.1 + - - +
304D GLU* 2.7 38.9 + - - +
327D SER 3.5 13.5 - - - +
328D LEU* 2.7 19.3 + - - +
330D ASN* 1.3 75.5 - - + +
332D VAL* 1.3 60.4 + - - +
334D GLN* 3.4 9.9 + - - +
335D ASP* 3.0 30.7 + - - +
842F T 4.6 1.6 + - - -
843F C 2.8 27.3 + - - -
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Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D PHE* 4.1 19.5 - - + -
328D LEU 3.1 11.4 + - - +
329D LEU* 3.7 10.3 - - + +
331D ARG* 1.3 76.0 - - - +
333D CYS* 1.3 54.5 + - - +
334D GLN 3.0 4.9 - - - -
335D ASP* 2.6 35.3 - - - +
336D GLY 4.7 0.2 - - - -
337D ARG 3.7 13.8 - - - +
338D LYS* 4.8 2.0 - - + -
339D PRO* 3.7 28.5 - - + -
371D LYS* 5.0 15.3 - - + -
410D PHE* 3.6 27.6 - - + -
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Residues in contact with CYS 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D LEU 3.1 15.1 + - - +
330D ASN* 3.3 13.2 + - - +
332D VAL* 1.3 76.5 - - - +
334D GLN* 1.3 57.2 + - + +
335D ASP 2.9 12.7 - - - +
371D LYS* 5.3 7.9 - - - -
372D LEU 4.5 17.3 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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