Contacts of the helix formed by residues 303 - 320 (chain D) in PDB entry 3ER8
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 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D ARG* 3.0 44.0 + - - -
142D LEU* 5.5 0.2 - - - +
143D ASN* 4.9 6.4 + - - -
301D ASP* 2.6 13.0 + - - +
302D PRO* 1.3 84.3 - - + +
304D LYS* 1.3 64.1 + - - +
305D PHE 3.3 2.5 - - - -
306D ASN* 3.1 31.1 + - - +
307D ALA* 3.9 2.9 + - - +
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Residues in contact with LYS 304 (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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294D ARG* 5.6 3.7 - - - +
297D ASP* 5.0 13.7 - - + +
298D LEU* 4.7 0.4 - - + -
301D ASP* 2.7 40.4 + - + +
303D GLU* 1.3 72.7 - - - +
305D PHE* 1.3 105.6 + - + +
306D ASN 3.6 0.2 + - - -
307D ALA* 4.0 12.8 + - - +
308D ARG* 4.2 15.8 + - + +
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Residues in contact with PHE 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LEU* 3.4 24.9 - - + +
285D MET* 3.7 33.2 - - + -
288D MET* 3.2 32.8 - - + -
289D PHE* 3.9 10.1 - + - -
294D ARG* 4.6 10.1 - - - -
297D ASP* 5.1 4.3 - - + -
298D LEU* 3.3 28.5 - - + +
303D GLU 3.3 0.4 - - - -
304D LYS* 1.3 118.0 - - + +
306D ASN* 1.3 58.8 + - - +
307D ALA 3.1 2.7 - - - -
308D ARG* 3.8 9.4 - - + +
309D MET* 2.5 40.4 + - + +
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Residues in contact with ASN 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU* 2.9 24.7 + - - +
138D ALA* 3.2 5.2 - - - +
139D ARG* 2.7 68.8 + - - +
142D LEU* 3.0 16.4 - - + +
303D GLU* 3.1 25.1 + - - +
305D PHE* 1.3 75.2 - - - +
307D ALA* 1.3 58.9 + - - +
310D ALA* 2.8 37.3 + - - +
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Residues in contact with ALA 307 (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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131D VAL* 5.0 2.5 - - - +
135D GLU* 6.3 1.3 - - - -
195D ASN* 4.8 1.0 + - - +
197D ASN 5.9 0.2 - - - +
198D ILE* 3.2 4.0 - - + +
303D GLU 3.9 3.3 + - - +
304D LYS 4.1 7.6 - - - +
306D ASN* 1.3 82.1 - - - +
308D ARG* 1.3 82.5 + - - +
310D ALA* 4.4 0.7 - - - +
311D THR* 2.5 35.0 + - - -
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Residues in contact with ARG 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D SER* 4.5 15.6 + - - +
191D LEU* 3.6 18.5 - - + +
197D ASN 4.5 2.4 + - - -
198D ILE* 2.7 59.7 - - - +
199D ARG* 3.3 44.9 + - - +
285D MET* 5.3 7.9 - - + -
304D LYS* 4.2 18.4 - - - +
305D PHE* 3.2 16.0 + - + +
307D ALA* 1.3 98.1 - - - +
309D MET* 1.3 62.1 + - - +
311D THR* 3.3 9.7 + - - -
312D MET* 3.2 23.8 + - - +
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Residues in contact with MET 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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138D ALA* 4.0 7.2 - - + +
141D MET* 4.8 8.7 - - - +
142D LEU* 3.2 27.8 - - + -
145D MET* 4.5 7.9 - - + -
282D LEU* 4.8 9.1 - - + +
285D MET* 4.0 17.6 - - + -
286D ILE* 6.5 0.7 - - + -
289D PHE* 3.0 43.7 - - + -
305D PHE* 2.5 32.3 + - + +
308D ARG* 1.3 70.3 - - - +
310D ALA* 1.3 59.7 + - - +
312D MET* 3.4 12.5 + - - +
313D LEU* 3.0 40.5 + - + +
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Residues in contact with ALA 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D VAL* 4.1 8.1 - - + +
134D MET* 3.6 25.8 - - - +
135D GLU* 3.9 11.0 - - + +
138D ALA* 3.4 17.4 - - + +
306D ASN 2.8 23.8 + - - +
307D ALA* 4.4 1.1 - - - +
309D MET* 1.3 68.4 - - - +
311D THR* 1.3 56.4 + - - +
312D MET 2.7 15.5 + - - -
313D LEU* 4.2 4.7 - - - +
314D GLU* 2.9 27.8 + - - +
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Residues in contact with THR 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D VAL* 3.2 19.7 - - + +
191D LEU* 4.0 17.0 - - + +
194D ILE* 4.1 15.0 - - + +
195D ASN* 3.2 32.8 + - + -
198D ILE* 2.9 22.0 - - + +
307D ALA 2.5 23.5 + - - -
308D ARG* 3.3 7.2 - - - -
310D ALA* 1.3 78.1 - - - +
312D MET* 1.3 55.9 + - - +
314D GLU* 4.0 2.6 - - - +
315D TYR* 3.7 18.0 + - - +
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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
----------------------------------------------------------
191D LEU* 3.7 34.8 - - + -
278D PRO* 3.9 11.2 - - + +
281D GLN* 4.2 8.7 - - - +
282D LEU* 3.5 58.7 - - + +
285D MET* 3.6 34.8 - - + -
308D ARG 3.2 17.9 + - - +
309D MET* 3.6 8.1 - - - +
310D ALA 2.7 1.8 + - - -
311D THR* 1.3 77.6 - - - +
313D LEU* 1.3 61.2 + - - +
314D GLU 2.9 5.6 - - - -
315D TYR* 3.0 17.9 + - - +
316D VAL* 3.1 11.1 + - - +
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Residues in contact with LEU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D MET* 4.0 8.5 - - + +
137D LEU* 3.8 26.0 - - + -
138D ALA* 4.0 11.0 - - + +
141D MET* 3.6 28.5 - - - -
282D LEU* 4.0 10.5 - - + -
309D MET* 3.0 37.1 + - + +
310D ALA 3.0 1.1 + - - +
312D MET* 1.3 74.6 - - - +
314D GLU* 1.3 57.6 + - - +
316D VAL* 3.4 7.5 - - - +
317D ARG* 3.2 27.2 + - - +
324D PHE* 3.6 17.3 - - + -
443D LEU* 3.5 32.5 - - + -
446D MET* 4.8 0.9 - - + -
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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
----------------------------------------------------------
130D ASN* 3.0 33.7 - - + +
131D VAL* 3.5 16.6 - - + +
133D SER* 2.8 20.5 + - - -
134D MET* 3.3 23.2 - - + +
310D ALA 2.9 17.3 + - - +
311D THR 4.0 5.8 - - - +
313D LEU* 1.3 78.8 - - - +
315D TYR* 1.3 61.1 + - - +
317D ARG* 2.7 35.4 + - - +
318D TYR* 3.6 17.3 + - - +
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Residues in contact with TYR 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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194D ILE* 4.2 25.4 - - + -
268D ILE* 3.6 32.2 - - + +
277D ASP* 4.4 0.8 + - - -
278D PRO* 3.7 40.8 - - + -
279D THR* 3.7 20.2 - - - -
311D THR 3.7 13.1 + - - +
312D MET* 3.0 11.7 + - - +
314D GLU* 1.3 78.2 - - - +
316D VAL* 1.3 61.5 + - - +
318D TYR* 3.4 2.6 + - - +
319D THR* 2.6 69.9 + - + +
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Residues in contact with VAL 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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279D THR* 4.3 13.2 - - + +
282D LEU* 4.2 10.5 - - + -
312D MET 3.1 9.5 + - - +
313D LEU* 3.4 16.6 - - - +
315D TYR* 1.3 84.2 - - + +
317D ARG* 1.3 77.2 + - - +
319D THR* 4.3 2.9 - - - -
320D HIS* 2.9 27.4 + - + -
322D ILE* 3.2 28.7 - - + +
324D PHE* 3.7 17.7 - - + -
439D LEU* 3.7 27.4 - - + -
443D LEU* 4.2 6.5 - - + -
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Residues in contact with ARG 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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133D SER* 4.9 4.2 + - - -
134D MET* 3.8 19.1 - - - -
313D LEU 3.2 17.4 + - - +
314D GLU* 2.7 36.7 + - - +
315D TYR 3.4 0.2 - - - -
316D VAL* 1.3 79.8 - - - +
318D TYR* 1.3 77.2 + - - +
321D GLY* 3.0 5.0 - - - -
322D ILE 2.9 30.9 + - - +
324D PHE* 3.5 20.2 - - + -
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Residues in contact with TYR 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* 3.6 11.5 + - - +
315D TYR* 3.4 6.8 + - - +
316D VAL 3.1 0.6 - - - -
317D ARG* 1.3 91.8 - - - +
319D THR* 1.3 62.3 + - - +
320D HIS 2.5 2.3 + - - -
321D GLY* 2.4 32.9 + - - -
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Residues in contact with THR 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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277D ASP* 5.8 1.3 - - - +
279D THR* 4.6 0.2 - - - +
315D TYR* 2.6 64.8 + - + +
316D VAL* 4.1 2.0 - - - -
318D TYR* 1.3 86.7 - - - +
320D HIS* 1.3 88.1 + - + +
321D GLY 3.6 0.2 - - - -
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Residues in contact with HIS 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ASP* 5.5 3.2 + - - -
279D THR* 4.2 20.7 + - + -
316D VAL* 2.9 14.7 + - + +
318D TYR 2.5 3.2 + - - -
319D THR* 1.3 102.3 + - + +
321D GLY* 1.3 66.7 + - - +
322D ILE* 2.9 21.3 + - + +
435D TYR* 3.6 15.7 + + - -
436D LYS* 3.0 42.9 + - + +
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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
------------------------------------------------------------
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