Contacts of the helix formed by residues 298 - 316 (chain D) in PDB entry 3M0V
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 GLU 298 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLU* 3.4 44.3 - - + +
300A TYR* 5.2 1.3 - - - -
284D ASP* 2.9 16.2 + - - +
285D SER 4.7 2.9 - - - +
286D LYS* 5.7 1.7 - - - -
297D ILE* 1.3 88.7 - - + +
299D PRO* 1.3 65.6 - - - +
300D TYR* 3.2 3.2 + - + +
301D ARG* 3.3 61.1 + - + +
302D LEU* 3.6 6.4 + - - +
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Residues in contact with PRO 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 3.7 19.1 - - + -
378A LYS* 4.2 4.7 - - - +
381A TYR* 3.8 18.6 - - + -
295D GLY* 3.6 27.1 - - - +
297D ILE 3.7 7.4 - - - +
298D GLU* 1.3 88.0 - - - +
300D TYR* 1.3 61.3 + - - +
302D LEU* 3.4 6.1 + - + +
303D PHE* 3.2 20.3 + - - +
345D GLU* 3.7 16.3 - - - +
349D ALA* 5.3 1.4 - - - +
381D TYR* 3.2 24.7 - - + +
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Residues in contact with TYR 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ALA 3.6 20.7 + - - -
297A ILE 3.3 22.2 - - - +
298A GLU* 5.3 0.7 - - - -
299A PRO* 3.7 26.5 - - + -
300A TYR* 6.4 0.2 - - + -
187B PRO* 4.1 12.7 - - + +
298D GLU* 3.2 1.4 - - + -
299D PRO* 1.3 76.6 - - - +
301D ARG* 1.3 59.8 + - - +
303D PHE* 3.1 28.7 + + - +
304D LEU* 2.8 54.5 + - + +
374D THR* 4.5 3.5 + - - -
377D LEU* 4.0 15.6 - - - +
378D LYS* 3.5 25.6 - - + +
381D TYR* 3.4 38.2 + + + -
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Residues in contact with ARG 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LYS* 6.2 2.2 - - - +
297A ILE 5.6 0.4 + - - -
255D LEU* 5.1 16.5 + - + +
262D THR 5.8 2.1 + - - -
264D ILE* 4.1 28.9 - - + +
265D GLU* 4.3 14.3 - - - +
283D ASN 5.5 0.4 + - - -
284D ASP* 2.8 29.1 + - - +
285D SER* 3.2 29.9 + - - +
298D GLU* 3.3 44.1 + - - +
300D TYR* 1.3 78.6 - - - +
302D LEU* 1.3 64.0 + - - +
304D LEU* 3.1 12.5 + - - +
305D VAL* 3.0 29.4 + - + +
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Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D LEU* 4.1 15.9 - - + -
282D PHE* 3.9 32.5 - - + -
283D ASN 5.7 0.2 - - - +
294D ALA* 4.5 8.1 - - + -
295D GLY* 4.2 14.8 - - - +
298D GLU 3.6 5.4 + - - +
299D PRO* 3.4 12.3 + - + +
300D TYR 3.2 0.2 - - - -
301D ARG* 1.3 79.9 - - - +
303D PHE* 1.3 63.5 + - - +
305D VAL* 3.3 7.8 + - + +
306D PHE* 3.2 34.0 + - + -
345D GLU* 3.8 43.1 - - + +
346D ILE* 4.3 6.7 - - + +
349D ALA* 3.8 11.2 - - + -
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Residues in contact with PHE 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D PRO 3.2 8.4 + - - +
300D TYR* 3.1 38.2 + + - +
302D LEU* 1.3 77.1 - - - +
304D LEU* 1.3 70.2 + - + +
306D PHE* 3.2 2.9 + - - +
307D ASN* 2.8 30.2 + - + +
349D ALA* 3.9 17.4 - - + +
352D GLN* 3.7 30.7 - - + +
353D ALA* 3.6 24.2 - - - -
356D VAL* 4.0 15.9 - - + -
377D LEU* 3.6 31.4 - - + -
381D TYR* 3.6 27.4 - + + -
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 5.3 2.7 - - + +
187B PRO* 3.9 26.0 - - + -
228B TYR* 3.8 10.1 - - + +
265D GLU* 3.6 32.9 - - + +
300D TYR* 2.8 44.1 + - + +
301D ARG* 3.1 9.8 + - - +
303D PHE* 1.3 96.1 - - + +
305D VAL* 1.3 63.7 + - - +
307D ASN* 3.4 9.9 + - - +
308D GLU* 3.4 22.9 + - - +
377D LEU* 4.0 11.7 - - + -
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Residues in contact with VAL 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D LEU* 4.4 18.8 - - + -
264D ILE* 4.8 3.6 - - + -
265D GLU* 4.2 26.5 - - + +
268D VAL* 4.3 6.2 - - + +
280D PHE* 3.9 34.8 - - + -
282D PHE* 4.6 12.8 - - + -
301D ARG* 3.0 22.4 + - + +
302D LEU* 3.6 11.9 - - + +
303D PHE 3.2 0.2 - - - -
304D LEU* 1.3 75.6 - - - +
306D PHE* 1.3 63.0 + - + +
308D GLU* 3.0 21.0 + - - +
309D LEU* 3.3 13.8 + - + +
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Residues in contact with PHE 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D PHE* 3.5 27.4 - + - -
282D PHE* 3.6 29.2 - + - -
302D LEU* 3.2 28.1 + - + +
303D PHE 3.7 6.3 - - - +
305D VAL* 1.3 76.8 - - + +
307D ASN* 1.3 61.0 + - - +
309D LEU* 3.6 24.9 - - + +
310D VAL* 2.9 33.4 + - - +
324D HIS* 4.2 0.4 - - - -
346D ILE* 3.4 38.6 - - + -
349D ALA* 3.7 25.1 - - + +
350D TYR* 3.9 23.6 - + + -
353D ALA* 3.9 5.6 - - + -
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Residues in contact with ASN 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLY* 5.5 2.2 - - - +
303D PHE* 2.8 21.7 + - + +
304D LEU* 3.5 17.0 + - - +
305D VAL 3.1 0.2 - - - -
306D PHE* 1.3 77.7 - - - +
308D GLU* 1.3 69.4 + - - +
311D ASP* 3.0 28.0 + - - +
353D ALA* 4.2 3.8 - - - -
356D VAL* 4.0 1.8 - - - +
358D ARG* 2.9 41.5 + - - +
361D LEU* 5.2 2.8 - - - +
377D LEU* 3.5 37.1 - - - +
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Residues in contact with GLU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASN* 5.7 1.0 - - - +
192B PHE* 3.4 32.6 + - - +
193B THR* 5.1 1.2 + - - -
265D GLU* 3.5 25.3 - - + +
268D VAL* 4.2 14.8 - - + -
269D ALA* 3.4 19.5 - - + +
272D ILE* 4.2 3.5 - - - +
304D LEU 3.4 11.7 + - - +
305D VAL 3.0 8.8 + - - +
307D ASN* 1.3 92.1 + - - +
309D LEU* 1.3 60.2 + - - +
311D ASP* 3.4 13.5 + - - +
312D ALA* 3.0 28.2 + - - +
315D ARG* 4.6 5.4 + - - -
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D VAL* 4.0 6.7 - - + -
272D ILE* 4.0 1.6 - - + -
277D LEU* 4.0 5.2 - - + -
280D PHE* 3.6 38.1 - - + -
282D PHE* 5.2 0.2 - - + -
305D VAL* 3.6 12.3 - - + +
306D PHE* 3.2 34.9 + - + +
308D GLU* 1.3 78.4 - - - +
310D VAL* 1.3 63.0 + - + +
312D ALA* 3.3 16.3 + - - +
313D GLU* 3.4 6.9 + - - +
320D PHE* 3.6 36.0 - - + -
322D PRO* 4.6 1.6 - - + -
324D HIS* 3.7 17.7 - - + +
350D TYR* 6.5 0.2 - - + -
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Residues in contact with VAL 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D PHE 2.9 18.8 + - - +
309D LEU* 1.3 74.3 - - + +
311D ASP* 1.3 65.8 - - - +
313D GLU* 3.1 15.3 + - + +
314D ALA* 2.9 19.9 + - + +
350D TYR* 4.5 14.4 - - + -
353D ALA* 3.6 23.6 - - + +
354D LEU* 4.1 27.6 - - + -
358D ARG* 3.5 32.3 - - + +
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Residues in contact with ASP 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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191B ASN* 3.0 29.7 + - - -
194B ARG* 4.5 2.6 + - - -
307D ASN* 3.0 21.6 + - - +
308D GLU* 3.7 13.7 - - - +
310D VAL* 1.3 76.6 - - - +
312D ALA* 1.3 51.9 + - - +
314D ALA* 3.0 12.0 + - - +
315D ARG* 2.7 70.0 + - - +
358D ARG* 3.9 17.8 + - - +
361D LEU* 6.0 0.9 - - - +
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Residues in contact with ALA 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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272D ILE* 4.1 13.2 - - + -
308D GLU 3.0 13.6 + - - +
309D LEU 3.3 11.4 - - - +
311D ASP* 1.3 78.2 - - - +
313D GLU* 1.3 62.4 + - - +
315D ARG* 3.3 12.6 + - - +
316D GLY 3.2 3.1 + - - -
317D VAL* 3.0 41.2 + - + +
320D PHE* 3.9 24.0 - - + -
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Residues in contact with GLU 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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46D LYS* 4.3 20.4 + - - +
309D LEU 3.4 6.3 + - - +
310D VAL* 3.1 17.4 + - + +
312D ALA* 1.3 78.7 - - - +
314D ALA* 1.3 57.7 + - - +
316D GLY* 3.0 20.8 + - - -
317D VAL 4.7 6.7 - - - +
320D PHE* 5.3 3.7 - - + -
350D TYR* 5.6 2.4 + - - -
354D LEU* 5.4 4.3 - - - +
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Residues in contact with ALA 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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194B ARG* 5.6 0.8 + - - -
310D VAL* 2.9 14.3 + - + +
311D ASP* 3.0 15.9 + - - +
313D GLU* 1.3 79.0 - - - +
315D ARG* 1.3 58.7 + - - +
316D GLY* 3.1 1.3 + - - -
358D ARG* 4.3 26.5 - - + -
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Residues in contact with ARG 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASN* 4.2 7.6 + - - -
193B THR* 3.7 36.3 + - - +
194B ARG* 3.9 39.1 + - - +
197B GLU* 6.1 0.4 - - - -
269D ALA* 5.9 1.2 - - - +
272D ILE* 4.0 17.6 - - - +
273D GLN* 5.0 4.2 - - - +
308D GLU* 4.6 7.5 + - - -
311D ASP* 2.7 65.5 + - - +
312D ALA* 3.7 16.3 - - - +
313D GLU 3.2 0.2 - - - -
314D ALA* 1.3 72.9 - - - +
316D GLY* 1.3 59.7 + - - +
317D VAL* 3.5 23.9 - - + +
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Residues in contact with GLY 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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313D GLU 3.0 14.2 + - - -
314D ALA 3.1 2.1 - - - -
315D ARG* 1.3 80.4 - - - +
317D VAL* 1.3 67.1 + - - +
318D LYS* 3.2 26.1 + - - +
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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