Contacts of the helix formed by residues 300 - 317 (chain B) in PDB entry 2D2O
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 ASN 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B ASP* 3.1 39.5 + - - +
267B TRP* 4.1 6.3 - - - +
297B ARG* 2.9 23.3 + - - +
298B THR 3.8 1.2 - - - +
299B GLU* 1.3 78.3 - - - +
301B PRO* 1.3 74.7 - - - +
302B GLU* 2.8 43.0 + - - +
303B VAL* 2.9 22.7 + - + +
304B LYS* 3.0 11.8 + - - +
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Residues in contact with PRO 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLU 3.4 7.8 - - - +
300B ASN* 1.3 90.2 - - - +
302B GLU* 1.3 60.7 + - + +
304B LYS* 3.8 20.5 - - + +
305B GLU* 2.9 30.2 + - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ARG* 4.4 18.0 + - - +
264B TYR* 5.5 0.2 - - - -
267B TRP* 2.7 47.0 + - + +
300B ASN* 2.8 22.9 + - - +
301B PRO* 1.3 76.6 - - + +
303B VAL* 1.3 56.6 + - - +
305B GLU* 3.3 13.8 + - - +
306B TYR* 3.0 28.4 + - - +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B TRP* 3.5 49.8 - - + +
296B LEU* 4.3 15.5 - - + -
297B ARG 3.4 29.6 - - - +
298B THR* 3.9 9.4 - - - +
300B ASN* 2.9 8.8 + - + +
302B GLU* 1.3 72.9 - - - +
304B LYS* 1.3 68.0 + - - +
306B TYR* 3.2 6.5 + - + +
307B LEU* 2.9 45.9 + - + +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A ARG* 6.4 0.2 - - - +
298B THR 3.8 13.2 + - - +
299B GLU 6.1 0.7 - - - -
300B ASN 3.0 14.5 + - - +
301B PRO* 3.8 16.6 - - - +
303B VAL* 1.3 76.0 - - - +
305B GLU* 1.3 58.2 + - - +
307B LEU 3.5 0.2 + - - -
308B PHE* 2.9 67.2 + - + -
333B ALA* 5.7 2.8 - - - +
334B PHE* 3.9 28.8 - - + +
337B GLU* 2.6 39.5 + - - +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PRO 2.9 19.2 + - - +
302B GLU* 3.4 13.3 - - - +
304B LYS* 1.3 78.5 - - - +
306B TYR* 1.3 63.5 + - - +
308B PHE* 3.3 6.6 + - - +
309B ASP* 3.0 38.7 + - - +
312B ARG* 4.5 1.9 + - - +
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Residues in contact with TYR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ASP* 5.0 1.9 + - - -
209B TYR* 4.3 10.0 + + - +
210B LEU* 3.4 25.4 - - + +
249B PHE* 3.7 24.8 - + - -
250B PHE* 3.4 35.6 - + - -
267B TRP* 3.9 24.9 - + + -
302B GLU 3.0 13.8 + - - +
303B VAL* 3.6 7.2 - - + +
305B GLU* 1.3 76.7 + - - +
307B LEU* 1.3 73.1 + - + +
309B ASP* 3.0 12.4 + - + +
310B VAL* 3.0 40.7 + - + +
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B TYR* 4.5 12.8 - - + -
242B PHE* 3.6 60.8 - - + +
249B PHE* 6.0 0.4 - - + -
296B LEU* 4.2 16.6 - - + -
298B THR* 4.1 7.4 - - + -
303B VAL* 2.9 38.3 + - + +
304B LYS 4.1 2.0 - - - +
306B TYR* 1.3 88.6 - - + +
308B PHE* 1.3 63.9 + - - +
310B VAL* 3.2 8.7 + - + +
311B ALA* 3.0 21.8 + - - +
334B PHE* 4.1 15.7 - - + -
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LYS* 2.9 48.4 + - + +
305B GLU* 3.6 7.0 - - - +
307B LEU* 1.3 76.9 - - - +
309B ASP* 1.3 57.7 + - - +
311B ALA* 3.2 6.7 + - - +
312B ARG* 2.9 43.7 + - - +
334B PHE* 3.5 52.3 - + - -
337B GLU* 3.9 21.1 - - + -
338B PHE* 3.6 26.2 - + - -
341B LEU* 3.6 22.5 - - + +
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Residues in contact with ASP 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 5.3 1.1 - - - -
305B GLU* 3.0 28.6 + - - +
306B TYR* 3.0 13.5 + - + +
308B PHE* 1.3 74.5 - - - +
310B VAL* 1.3 66.9 + - - +
312B ARG* 2.8 32.3 + - - +
313B PHE* 2.9 24.5 + - - +
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 4.7 3.4 - - + -
209B TYR* 3.7 38.8 - - + +
210B LEU* 4.0 17.5 - - + -
242B PHE* 4.4 10.3 - - + -
306B TYR* 3.0 45.6 + - + +
307B LEU* 3.3 12.6 - - + +
309B ASP* 1.3 78.0 - - + +
311B ALA* 1.3 63.8 + - - +
313B PHE* 3.3 1.4 + - - +
314B TRP* 3.1 43.6 + - + +
322B TRP* 5.4 1.1 - - + -
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 4.6 3.1 - - + -
307B LEU 3.0 13.3 + - - +
308B PHE* 3.4 10.8 - - - +
310B VAL* 1.3 78.3 - - - +
312B ARG* 1.3 62.4 + - - +
314B TRP 3.5 0.2 + - - -
315B MET* 3.1 33.1 + - - +
322B TRP* 3.5 23.1 - - + +
338B PHE* 3.8 28.7 - - + -
341B LEU* 5.0 4.5 - - + -
342B VAL* 5.4 0.7 - - + -
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLU* 4.5 2.8 + - - +
308B PHE* 2.9 41.6 + - - +
309B ASP* 2.8 40.1 + - - +
311B ALA* 1.3 76.1 - - - +
313B PHE* 1.3 62.5 + - - +
315B MET* 3.3 2.8 + - - +
316B GLU* 3.0 36.1 + - + +
341B LEU* 3.7 30.4 - - + +
345B LEU* 4.0 29.3 - - + +
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B LEU* 3.7 37.0 - - + -
219B LEU* 4.2 19.3 - - + -
223B ARG* 5.8 0.2 - - - -
309B ASP 2.9 12.7 + - - +
310B VAL 3.3 7.8 + - - +
312B ARG* 1.3 76.3 - - - +
314B TRP* 1.3 105.6 + + - +
316B GLU* 3.1 21.1 + - - +
317B GLN* 3.0 41.9 + - - -
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Residues in contact with TRP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B PHE* 3.2 37.1 - + - -
209B TYR 2.8 26.7 + - - -
210B LEU* 3.8 10.3 - - - +
211B ALA 4.0 0.9 - - - -
212B ILE* 3.5 41.1 - - + -
219B LEU* 3.9 12.8 - - + -
222B PHE* 3.8 24.7 - + - -
238B LEU* 4.5 4.5 - - + -
310B VAL* 3.1 32.3 + - + +
313B PHE* 1.3 98.0 - + - +
315B MET* 1.3 62.0 + - - +
317B GLN* 2.8 34.7 + - + +
318B GLY 3.6 1.0 + - - -
319B ILE* 3.6 17.5 + - + +
322B TRP* 3.7 20.4 - + + -
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B ALA* 3.1 23.7 + - - +
312B ARG* 3.8 5.2 - - - +
313B PHE 3.3 0.2 - - - -
314B TRP* 1.3 76.8 - - - +
316B GLU* 1.3 61.3 + - + +
318B GLY* 3.0 14.4 + - - -
319B ILE* 3.7 17.7 + - + +
321B GLY 6.2 0.7 - - - +
322B TRP* 3.7 27.6 - - + +
341B LEU* 6.0 0.2 - - - -
342B VAL* 3.4 48.0 - - + +
345B LEU* 3.8 28.5 - - + -
346B ASN* 3.8 17.9 - - + +
349B ALA* 3.9 6.7 - - + -
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ARG* 4.9 3.6 + - - -
312B ARG* 3.0 30.9 + - - +
313B PHE* 3.1 24.7 - - - +
314B TRP 3.0 0.4 - - - -
315B MET* 1.3 79.3 - - - +
317B GLN* 1.3 62.7 + - - +
318B GLY* 3.2 4.0 + - - -
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Residues in contact with GLN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B LEU* 3.8 15.0 - - + +
222B PHE* 3.9 19.1 - - + -
223B ARG* 2.7 57.8 + - + +
226B VAL* 3.9 17.9 - - - +
313B PHE* 3.0 45.6 + - + +
314B TRP* 2.8 30.6 + - + +
316B GLU* 1.3 84.8 + - - +
318B GLY* 1.3 59.0 + - - +
319B ILE 3.7 0.9 - - - -
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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