Contacts of the helix formed by residues 305 - 321 (chain D) in PDB entry 3G2G
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 LYS 305 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 3.2 41.6 + - + +
36C ASP 5.7 0.2 - - - -
37C SER 4.7 4.0 + - - -
38C PRO* 4.8 4.2 - - - +
39C PRO* 4.6 7.7 - - - +
384C GLU* 2.7 42.9 + - - +
301D ILE* 4.0 11.7 - - + -
302D PRO* 2.9 42.2 + - + +
304D GLU* 1.3 81.1 - - + +
306D VAL* 1.3 64.6 + - - +
307D PHE 3.2 3.1 - - - -
308D LEU* 3.0 27.4 + - + +
309D ALA 3.4 4.0 + - - -
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Residues in contact with VAL 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C ARG* 4.9 10.1 - - + +
292D VAL* 5.5 0.2 - - + -
294D ARG* 4.0 39.9 - - + +
297D LEU* 4.3 9.9 - - + -
298D GLY* 3.4 35.9 - - - +
301D ILE* 4.4 9.4 - - + -
302D PRO 4.1 2.9 - - - +
303D ALA* 3.2 19.8 + - - +
305D LYS* 1.3 78.8 - - - +
307D PHE* 1.3 59.9 + - - +
309D ALA* 3.1 6.0 + - - +
310D GLN* 2.9 26.1 + - + +
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Residues in contact with PHE 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 5.6 0.2 - - + -
345C GLY 5.1 2.5 - - - +
346C SER* 4.8 14.8 - - - +
349C ALA* 3.5 30.7 - - + -
350C ASN* 5.6 0.9 - - - +
353C LEU* 4.4 5.6 - - + -
381C ILE* 4.5 4.9 - - + -
384C GLU* 3.8 10.3 - - + -
385C ALA* 3.4 31.6 - - + -
388C ALA* 4.0 11.9 - - + -
303D ALA 4.9 0.6 + - - -
304D GLU* 3.2 25.8 - - - -
306D VAL* 1.3 80.6 - - - +
308D LEU* 1.3 90.2 + - + +
310D GLN* 3.8 10.9 - - - +
311D LYS* 3.0 48.4 + - + +
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Residues in contact with LEU 308 (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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17C GLN* 3.8 24.7 - - - +
33C LEU* 3.9 24.9 - - + +
34C ASP 4.2 6.5 - - - +
35C ILE* 4.0 17.5 - - + +
384C GLU* 3.5 28.0 - - + +
388C ALA* 3.8 18.6 - - + -
305D LYS* 3.0 22.3 + - + +
307D PHE* 1.3 105.7 - - + +
309D ALA* 1.3 60.0 + - - +
311D LYS* 3.4 0.3 + - - -
312D MET* 2.9 31.5 + - - +
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Residues in contact with ALA 309 (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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35C ILE* 3.9 17.7 - - + +
277D VAL* 4.3 9.2 - - + -
297D LEU* 3.7 17.0 - - + -
301D ILE* 4.9 0.9 - - + -
305D LYS 3.4 3.0 + - - +
306D VAL* 3.1 8.8 + - - +
308D LEU* 1.3 79.0 - - - +
310D GLN* 1.3 57.9 + - - +
312D MET* 3.6 7.9 - - - +
313D MET* 2.8 56.1 + - + +
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Residues in contact with GLN 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C SER* 5.3 6.6 + - - -
350C ASN* 6.0 1.0 - - - +
292D VAL* 4.0 22.6 - - + +
294D ARG* 3.1 34.8 + - - +
306D VAL* 2.9 16.5 + - - +
307D PHE* 3.8 10.9 - - - +
309D ALA* 1.3 77.1 - - - +
311D LYS* 1.3 60.4 + - + +
313D MET* 3.8 0.7 - - - +
314D ILE* 2.9 49.8 + - + +
326D CYS* 3.8 20.8 - - - -
347D ASP* 5.0 1.8 + - - -
350D ASN* 5.1 0.6 - - - +
351D ALA* 3.9 14.3 - - - +
354D ASP* 3.0 21.8 + - - +
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Residues in contact with LYS 311 (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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26C PHE* 6.3 0.8 - - - -
30C MET* 3.3 28.4 - - + +
33C LEU* 3.8 22.0 - - + -
350C ASN* 3.0 31.1 + - - +
353C LEU* 3.6 25.0 - - + +
307D PHE* 3.0 39.7 + - + +
310D GLN* 1.3 75.8 - - + +
312D MET* 1.3 66.7 + - - +
314D ILE* 4.6 1.6 - - - -
315D GLY* 2.9 20.1 + - - -
350D ASN* 5.4 0.4 + - - -
354D ASP* 2.8 43.0 + - - +
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Residues in contact with MET 312 (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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30C MET 3.2 13.7 + - - +
31C CYS* 3.5 21.2 - - - +
33C LEU 3.6 20.2 - - - +
277D VAL* 3.8 37.7 - - + +
280D PHE* 4.0 8.7 - - + -
308D LEU 2.9 18.1 + - - +
309D ALA* 3.6 6.3 - - - +
311D LYS* 1.3 77.6 - - - +
313D MET* 1.3 78.3 + - + +
315D GLY* 3.7 0.7 - - - -
316D ARG* 2.9 66.7 + - - +
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Residues in contact with MET 313 (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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271D ILE* 3.6 40.8 - - + +
277D VAL* 4.1 5.2 - - + -
280D PHE* 3.4 34.3 - - + -
290D ILE* 4.3 4.5 - - + -
292D VAL* 4.1 27.4 - - + -
297D LEU* 4.0 12.3 - - + -
309D ALA* 2.8 47.5 + - + +
310D GLN 4.0 2.0 - - - +
312D MET* 1.3 82.6 - - + +
314D ILE* 1.3 61.5 + - - +
316D ARG* 3.8 0.7 - - - +
317D CYS* 2.9 36.0 + - - -
324D VAL* 4.5 0.4 - - - -
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Residues in contact with ILE 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C MET* 4.8 0.2 - - + -
292D VAL* 4.4 3.8 - - + -
310D GLN* 2.9 46.1 + - + +
311D LYS 4.2 2.0 - - - +
313D MET* 1.3 77.4 - - - +
315D GLY* 1.3 63.2 + - - +
317D CYS* 3.4 0.5 + - - +
318D ASN* 3.0 26.1 + - - +
324D VAL* 4.0 25.1 - - + -
326D CYS* 4.9 5.2 - - + -
351D ALA 4.3 0.2 - - - +
354D ASP* 3.3 44.9 - - + +
355D GLY* 3.4 22.9 - - - +
356D ALA* 3.6 17.3 - - + +
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Residues in contact with GLY 315 (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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27C LEU* 3.7 19.4 - - - +
30C MET* 4.2 10.5 - - - +
31C CYS* 3.4 12.7 - - - -
311D LYS 2.9 17.9 + - - -
312D MET 3.7 0.7 - - - -
314D ILE* 1.3 77.8 - - - +
316D ARG* 1.3 55.9 + - - +
318D ASN* 3.2 6.7 + - - +
319D ARG* 3.0 27.4 + - - +
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Residues in contact with ARG 316 (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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31C CYS* 2.9 37.3 + - + +
32C ARG* 4.7 4.6 - - - +
33C LEU 5.1 1.6 + - - -
277D VAL 5.3 1.4 + - - -
278D ARG 5.8 1.6 + - - -
280D PHE* 3.7 25.0 - - + +
281D ASP* 2.9 39.3 + - - +
284D LEU* 3.7 7.1 - - + +
312D MET* 2.9 45.8 + - - +
313D MET 4.0 0.2 - - - +
315D GLY* 1.3 75.3 - - - +
317D CYS* 1.3 57.0 + - - +
319D ARG* 3.4 28.0 + - - +
320D ALA* 3.0 28.1 + - - +
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Residues in contact with CYS 317 (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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280D PHE* 4.0 8.1 - - - -
284D LEU* 4.0 12.1 - - - -
290D ILE* 3.6 33.2 - - - -
313D MET 2.9 24.3 + - - +
314D ILE 3.9 1.8 - - - +
316D ARG* 1.3 74.7 - - - +
318D ASN* 1.3 60.8 + - - +
319D ARG 3.1 0.4 - - - -
320D ALA* 3.2 1.0 + - - +
321D GLY 2.8 25.1 + - - -
322D LYS 3.0 28.8 + - - +
323D PRO 4.4 1.8 - - - -
324D VAL* 3.6 25.8 - - + -
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Residues in contact with ASN 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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27C LEU* 4.6 10.6 - - + +
314D ILE* 3.0 23.2 + - - +
315D GLY* 3.5 7.9 - - - +
317D CYS* 1.3 77.5 - - - +
319D ARG* 1.3 61.6 + - - +
321D GLY* 3.5 10.1 + - - +
322D LYS 5.1 0.4 + - - -
324D VAL* 4.2 6.3 - - - +
354D ASP 3.7 5.7 - - - +
355D GLY* 3.2 41.0 + - - -
357D ASP* 4.3 0.8 + - - -
394D LEU* 5.4 8.7 - - + +
398D LEU* 3.9 21.5 - - + +
443D ARG* 4.5 8.8 + - - +
445D ARG* 3.4 23.2 + - + +
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Residues in contact with ARG 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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27C LEU* 4.8 14.8 - - + -
28C GLU* 2.9 38.3 + - - -
31C CYS* 3.6 20.5 - - - +
281D ASP* 4.7 6.5 + - - -
315D GLY 3.0 16.0 + - - +
316D ARG* 3.6 33.6 + - - +
317D CYS 3.1 0.4 - - - -
318D ASN* 1.3 78.9 - - - +
320D ALA* 1.3 57.0 + - - +
398D LEU* 5.1 2.0 - - - -
401D LEU* 5.1 21.2 - - + +
443D ARG* 2.8 20.1 + - - -
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Residues in contact with ALA 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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284D LEU* 3.7 24.5 - - + -
316D ARG 3.0 17.7 + - - +
317D CYS* 3.2 3.8 + - - +
319D ARG* 1.3 78.8 - - - +
321D GLY* 1.3 60.2 + - - +
322D LYS* 3.5 12.7 + - + +
443D ARG* 3.5 12.2 + - - +
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Residues in contact with GLY 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 CYS 2.8 6.4 + - - -
318D ASN* 3.5 7.2 + - - -
319D ARG 3.3 3.6 - - - -
320D ALA* 1.3 78.7 - - - +
322D LYS* 1.3 62.4 + - - +
439D HIS* 5.5 1.7 - - - +
443D ARG* 3.5 33.0 - - - +
466D TYR* 4.0 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
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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