Contacts of the helix formed by residues 300 - 312 (chain D) in PDB entry 2Y1X
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 ASP 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298D PHE* 3.9 19.9 - - + -
299D THR* 1.3 75.5 - - - +
301D GLU* 1.3 62.3 + - - +
302D GLN* 3.5 9.5 + - - +
303D LEU* 2.9 29.3 + - + +
304D TYR* 3.3 16.1 + - - +
344D PHE* 5.4 1.2 - - - +
348D ILE* 4.6 9.7 - - + +
386D HIS* 3.0 16.2 + - - +
420D ARG* 2.9 23.5 + - - +
476D ARG* 4.9 5.1 + - - -
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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
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299D THR* 4.1 1.0 + - - +
300D ASP* 1.3 73.2 + - - +
302D GLN* 1.3 65.2 + - + +
304D TYR* 3.4 7.3 + - - +
305D MET* 3.1 57.7 + - + +
384D LEU* 3.7 18.3 - - - +
386D HIS* 3.1 30.4 + - + -
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Residues in contact with GLN 302 (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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300D ASP* 3.3 6.9 + - - +
301D GLU* 1.3 79.1 + - + +
303D LEU* 1.3 64.8 + - - +
305D MET* 3.3 15.6 + - + +
306D GLU* 2.9 26.8 + - - +
476D ARG* 5.2 4.0 - - - +
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Residues in contact with LEU 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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298D PHE* 4.0 11.4 - - + -
300D ASP* 2.9 27.3 + - - +
302D GLN* 1.3 73.5 - - - +
304D TYR* 1.3 60.2 + - - +
306D GLU* 3.4 6.3 - - - +
307D GLN* 2.7 39.7 + - - +
340D VAL* 4.3 15.5 - - + -
420D ARG* 3.6 31.4 - - + +
422D LEU* 3.9 24.9 - - + -
476D ARG* 3.3 48.1 - - - +
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Residues in contact with TYR 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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300D ASP 3.3 5.7 + - - +
301D GLU* 3.6 11.4 - - - +
302D GLN 3.2 0.4 - - - -
303D LEU* 1.3 80.0 - - - +
305D MET* 1.3 73.7 + - + +
307D GLN* 3.0 24.1 + - - +
308D PHE* 3.2 33.1 - + - -
336D PHE* 3.8 9.6 - + - -
386D HIS* 3.7 35.0 - + + +
422D LEU* 4.3 19.4 - - + +
423D PHE 3.5 21.3 - - - -
424D GLN 2.8 19.6 + - - -
425D SER* 3.6 1.9 - - - -
426D PRO* 3.4 27.9 - - + +
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Residues in contact with MET 305 (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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301D GLU* 3.1 51.0 + - + +
302D GLN* 4.1 14.8 - - + +
304D TYR* 1.3 88.5 - - + +
306D GLU* 1.3 62.5 + - - +
308D PHE* 2.9 22.8 + - + +
309D THR* 3.0 18.1 + - - +
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Residues in contact with GLU 306 (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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302D GLN 2.9 17.2 + - - +
303D LEU* 3.4 6.8 - - - +
304D TYR 3.1 0.2 - - - -
305D MET* 1.3 77.9 - - - +
307D GLN* 1.3 69.0 + - - +
309D THR* 3.2 10.6 + - - -
310D LYS* 3.0 49.4 + - + +
474D PHE* 4.5 5.5 - - - -
476D ARG* 3.1 42.5 + - - -
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Residues in contact with GLN 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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303D LEU* 2.7 38.0 + - - +
304D TYR 3.2 14.1 - - - +
306D GLU* 1.3 88.1 + - - +
308D PHE* 1.3 57.7 + - + +
310D LYS* 3.6 16.2 + - - +
311D ALA* 3.2 25.7 + - - +
332D VAL* 5.3 1.7 - - - -
335D TYR* 3.6 32.4 - - + +
336D PHE* 3.7 30.5 - - + -
422D LEU* 3.8 24.5 - - + +
474D PHE* 6.1 1.7 - - - -
476D ARG* 5.7 0.4 - - - +
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Residues in contact with PHE 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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304D TYR* 3.2 50.9 - + - -
305D MET* 2.9 11.4 + - + +
307D GLN* 1.3 73.5 - - - +
309D THR* 1.3 66.1 + - - +
310D LYS 3.0 1.6 - - - -
311D ALA* 4.3 4.0 - - - +
312D ASN* 2.8 33.3 + - - +
328D ARG* 3.4 33.7 - - - +
332D VAL* 3.8 23.1 - - + -
336D PHE* 3.8 23.8 - + - -
424D GLN 5.1 1.6 - - - -
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Residues in contact with THR 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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305D MET* 3.0 18.9 + - - +
306D GLU* 3.2 13.5 + - - -
308D PHE* 1.3 77.2 - - - +
310D LYS* 1.3 63.4 + - + +
312D ASN* 3.6 15.8 + - - +
313D PHE 4.1 2.6 + - - -
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Residues in contact with LYS 310 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B GLN* 4.2 8.6 + - - +
306D GLU* 3.0 41.2 + - + +
307D GLN* 3.8 14.8 + - - +
308D PHE 3.0 0.6 - - - -
309D THR* 1.3 76.9 - - + +
311D ALA* 1.3 65.4 + - - +
312D ASN 3.1 1.3 - - - -
313D PHE* 3.0 23.2 + - - +
335D TYR* 3.3 46.3 - - + +
474D PHE* 3.8 35.3 - - - -
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Residues in contact with ALA 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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307D GLN 3.2 14.6 + - - +
308D PHE* 3.1 4.6 + - - +
310D LYS* 1.3 78.5 - - - +
312D ASN* 1.3 59.7 + - - +
313D PHE 3.0 0.7 - - - -
314D TRP* 3.0 30.4 + - - +
328D ARG* 3.7 9.1 - - - +
331D ALA* 4.0 10.0 - - + +
332D VAL* 3.6 41.7 - - + +
335D TYR* 3.7 8.0 - - + -
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Residues in contact with ASN 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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308D PHE* 2.8 24.8 + - - +
309D THR* 3.8 11.1 - - - +
310D LYS 3.1 0.6 - - - -
311D ALA* 1.3 71.7 - - - +
313D PHE* 1.3 67.8 + - - +
314D TRP 2.9 1.8 - - - -
315D TYR* 2.8 34.9 + - + +
316D GLN* 4.7 1.6 + - - -
328D ARG* 2.8 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
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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