Contacts of the helix formed by residues 297 - 314 (chain D) in PDB entry 6E90
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 LEU 297 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209D VAL* 5.2 1.1 - - + -
269D ARG* 3.6 40.4 - - + -
270D ASN* 3.2 36.8 - - - +
273D VAL* 3.5 37.2 - - + -
274D ALA 5.3 0.2 - - - +
284D ILE* 4.9 2.7 - - + -
288D GLU* 2.7 24.8 + - + +
292D LEU* 3.8 9.2 - - + -
295D GLN 3.6 0.8 + - - -
296D LYS* 1.3 75.4 - - - +
298D GLN* 1.3 64.9 + - - +
299D GLY 3.5 0.4 + - - -
300D PRO* 3.8 24.4 - - + +
301D GLU* 3.8 13.2 + - - +
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Residues in contact with GLN 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ASN* 4.3 17.3 - - - +
270D ASN* 4.1 3.3 + - - +
296D LYS* 3.9 3.5 + - - +
297D LEU* 1.3 74.9 - - - +
299D GLY* 1.3 55.9 + - - +
301D GLU* 3.2 6.1 + - - +
302D THR* 2.7 44.6 + - - +
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Residues in contact with GLY 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ASN* 3.6 29.3 - - - +
206D VAL* 3.6 12.0 - - - +
209D VAL* 4.3 4.0 - - - -
270D ASN* 2.9 18.1 + - - -
298D GLN* 1.3 77.6 - - - +
300D PRO* 1.3 67.2 - - - +
302D THR* 3.3 0.6 + - - -
303D ALA* 3.0 19.6 + - - +
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Residues in contact with PRO 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D VAL* 3.8 15.5 - - + -
270D ASN* 3.6 9.0 - - - +
284D ILE* 4.0 34.8 - - + -
297D LEU* 3.8 17.7 - - + +
299D GLY* 1.3 88.4 - - - +
301D GLU* 1.3 63.0 + - - +
303D ALA* 3.1 7.4 + - + +
304D ARG 3.1 18.7 + - - -
325D VAL* 5.2 0.7 - - + -
329D CYS* 4.0 13.7 - - - -
330D TYR* 3.2 33.4 - - + +
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Residues in contact with GLU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ARG* 5.7 0.5 - - - -
326B TYR* 5.6 3.5 + - - -
330B TYR* 5.6 2.1 - - - +
296D LYS* 6.3 1.3 - - + -
297D LEU 3.8 12.2 + - - +
298D GLN* 3.2 10.6 + - - +
300D PRO* 1.3 79.8 - - - +
302D THR* 1.3 61.0 + - - +
304D ARG* 2.8 40.0 + - - +
305D GLU* 2.9 52.1 + - - +
330D TYR* 3.5 5.4 + - - +
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Residues in contact with THR 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D VAL* 4.6 12.7 - - + +
129D LEU* 4.6 13.9 - - + -
202D ALA* 4.1 25.6 + - + +
203D LEU* 4.6 4.7 - - + -
206D VAL* 3.8 17.7 - - + -
298D GLN* 2.7 29.2 + - - +
299D GLY* 3.7 4.0 - - - -
301D GLU* 1.3 74.8 - - - +
303D ALA* 1.3 56.7 + - - +
305D GLU* 3.1 7.8 + - - +
306D LEU* 2.8 39.0 + - + +
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Residues in contact with ALA 303 (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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206D VAL* 3.9 23.1 - - + +
299D GLY 3.0 13.3 + - - +
300D PRO* 3.1 10.0 + - + +
302D THR* 1.3 76.6 - - - +
304D ARG* 1.3 55.8 - - - +
306D LEU* 3.3 8.6 + - - +
307D TYR* 3.0 26.7 + - - +
322D PHE 4.2 2.2 - - - +
323D MET* 4.0 1.7 - - - +
325D VAL* 4.0 6.7 - - + -
326D TYR* 3.9 32.4 - - + +
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Residues in contact with ARG 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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301B GLU* 3.8 9.9 + - - -
304B ARG* 3.2 55.1 - - - +
330B TYR* 4.1 21.0 - - - -
300D PRO 3.1 11.0 + - - +
301D GLU* 2.8 40.2 + - - +
303D ALA* 1.3 77.4 - - - +
305D GLU* 1.3 61.7 + - + +
307D TYR* 3.3 5.6 + - + +
308D SER* 3.3 20.6 + - - -
326D TYR* 3.6 20.3 - - + -
330D TYR* 3.5 47.5 + - + -
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Residues in contact with GLU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLN* 5.1 5.9 - - - +
326B TYR* 5.6 2.2 + - - -
122D VAL* 5.9 2.9 - - - +
123D ASP 5.5 2.4 - - - +
129D LEU* 4.3 26.3 + - + +
301D GLU* 2.9 40.7 + - - +
302D THR* 3.1 7.4 + - - +
304D ARG* 1.3 75.1 - - + +
306D LEU* 1.3 64.4 + - - +
308D SER* 3.3 8.1 + - - +
309D ILE* 3.0 28.9 + - + +
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Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LEU* 4.6 11.4 - - + -
203D LEU* 3.8 24.5 - - + -
206D VAL* 4.2 16.4 - - + -
238D PHE* 3.3 42.8 - - + -
302D THR* 2.8 25.8 + - + +
303D ALA* 3.6 7.0 - - - +
305D GLU* 1.3 69.4 - - - +
307D TYR* 1.3 60.8 + - - +
309D ILE* 3.3 4.3 + - + +
310D LEU* 2.8 38.8 + - + +
322D PHE* 3.8 28.0 - - + -
323D MET* 4.1 9.9 - - + -
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Residues in contact with TYR 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASP* 5.1 7.5 + - - -
124B GLU* 5.2 6.1 - - + -
304B ARG* 6.0 2.2 - - - -
305B GLU* 5.8 3.4 - - - -
303D ALA 3.0 13.2 + - - +
304D ARG* 3.4 11.0 - - + +
305D GLU 3.3 0.2 - - - -
306D LEU* 1.3 77.3 - - - +
308D SER* 1.3 62.5 + - - +
310D LEU* 3.3 1.2 + - - +
311D GLN* 2.9 63.6 + - + +
316D VAL* 4.0 23.1 - - + -
323D MET* 3.6 28.4 - - - +
326D TYR* 3.5 44.9 - + + -
327D LYS* 6.0 2.2 - - + -
331D GLU* 5.0 8.1 + - - -
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Residues in contact with SER 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU* 2.8 26.1 + - - -
304B ARG* 4.7 8.5 + - - -
308B SER* 3.4 25.7 + - - -
304D ARG 3.3 9.7 + - - -
305D GLU* 3.3 11.4 + - - -
306D LEU 3.2 0.8 - - - -
307D TYR* 1.3 78.2 - - - +
309D ILE* 1.3 67.3 + - - +
311D GLN* 3.1 6.3 + - - +
312D HIS* 3.1 29.7 + - - -
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Residues in contact with ILE 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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129D LEU* 3.8 35.9 - - + +
238D PHE* 4.3 18.6 - - + -
242D PHE* 4.0 26.5 - - + -
305D GLU* 3.0 20.0 + - + +
306D LEU* 3.7 6.3 - - - +
308D SER* 1.3 75.1 - - - +
310D LEU* 1.3 64.3 + - + +
312D HIS* 3.3 19.7 + - - +
313D LYS* 3.4 39.9 + - + +
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Residues in contact with LEU 310 (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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238D PHE* 4.1 22.4 - - + -
241D LEU* 5.0 7.4 - - + -
306D LEU* 2.8 27.9 + - + +
307D TYR 3.9 3.1 - - - +
309D ILE* 1.3 72.1 - - + +
311D GLN* 1.3 60.8 + - - +
313D LYS* 3.3 3.3 + - + +
314D GLY 2.9 8.7 + - - -
315D LEU* 2.9 40.4 + - + +
316D VAL* 3.8 17.4 + - + +
319D PHE* 3.6 48.9 - - + -
322D PHE* 5.3 1.3 - - + -
323D MET* 3.8 28.3 - - + -
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Residues in contact with GLN 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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123B ASP* 5.3 5.3 + - - +
124B GLU* 3.2 42.8 + - + +
125B GLY* 3.4 16.4 - - - -
126B PRO* 3.5 4.3 - - - +
307D TYR* 2.9 52.8 + - + +
308D SER 3.1 8.0 + - - +
310D LEU* 1.3 78.0 - - - +
312D HIS* 1.3 61.7 + - - +
313D LYS 3.1 0.9 + - - -
314D GLY* 3.2 11.4 + - - +
316D VAL* 3.3 20.4 - - + +
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Residues in contact with HIS 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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124B GLU* 2.9 32.8 + - + +
125B GLY 3.1 26.2 - - - +
126B PRO* 3.2 22.5 - - - +
128B GLY* 3.8 19.1 + - - -
308B SER* 3.7 12.1 + - - -
309B ILE* 4.8 1.4 - - - +
312B HIS* 3.8 45.1 + - + +
308D SER* 3.1 18.0 + - - -
309D ILE* 3.3 10.4 + - + +
311D GLN* 1.3 75.6 - - - +
313D LYS* 1.3 59.7 + - + +
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Residues in contact with LYS 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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126B PRO* 5.0 3.1 - - - -
238D PHE* 5.2 0.2 - - - -
241D LEU* 3.2 44.4 - - + +
242D PHE* 3.7 18.1 - - - +
309D ILE* 3.4 37.7 - - + +
310D LEU* 3.3 6.0 + - + +
311D GLN 3.1 0.6 - - - -
312D HIS* 1.3 80.5 - - + +
314D GLY* 1.3 60.9 + - - +
315D LEU* 3.5 21.3 - - + +
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Residues in contact with GLY 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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126B PRO* 4.6 9.8 - - - +
310D LEU 2.9 5.1 + - - -
311D GLN* 3.2 11.5 + - - -
313D LYS* 1.3 80.0 - - - +
315D LEU* 1.3 64.6 + - - +
316D VAL 3.7 2.8 + - - -
317D ASP 5.4 0.2 + - - -
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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