Contacts of the helix formed by residues 308 - 318 (chain D) in PDB entry 2Y05
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 308 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C ASN* 2.9 36.5 + - - +
75C LYS 3.9 13.0 + - - +
77C VAL* 4.6 14.6 - - + +
303D ILE* 3.6 19.7 - - + +
304D GLU 2.8 24.5 + - - -
305D GLY* 2.9 9.7 + - - +
307D GLU* 1.3 80.6 - - - +
309D MET* 1.3 63.6 + - - +
310D PRO* 3.3 3.4 - - - -
311D ALA* 3.2 11.6 + - + +
312D ALA* 2.9 20.8 + - - +
327D VAL* 5.1 0.2 - - - -
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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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7D TRP* 4.0 4.0 - - + -
44D LEU* 3.6 40.2 - - + -
45D THR 3.5 25.4 - - - +
46D VAL* 3.9 7.0 - - + +
66D GLN 5.6 0.4 - - - +
90D GLY 5.7 0.2 - - - -
91D TRP* 3.5 50.9 - - + +
305D GLY 3.8 0.8 + - - -
306D PHE* 3.1 25.7 + - - +
308D ASN* 1.3 76.1 - - - +
310D PRO* 1.3 69.7 - - + +
312D ALA* 3.0 4.2 + - - +
313D PHE* 3.0 20.8 + - - +
327D VAL* 3.9 22.4 - - + -
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Residues in contact with PRO 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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7D TRP* 3.4 51.4 - - + +
19D ASN* 5.4 1.6 - - - +
22D PHE* 3.8 27.8 - - + -
91D TRP* 3.9 15.5 - - + -
307D GLU 4.0 1.8 - - - +
308D ASN 3.5 2.9 - - - -
309D MET* 1.3 94.5 - - + +
311D ALA* 1.3 57.6 + - - +
313D PHE* 3.1 5.5 + - + +
314D MET* 2.8 40.4 + - + +
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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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77C VAL* 4.3 28.2 - - + +
19D ASN* 5.4 2.7 + - - +
308D ASN* 3.2 15.5 + - + +
310D PRO* 1.3 79.7 - - - +
312D ALA* 1.3 57.6 + - - +
314D MET* 3.8 12.4 - - + +
315D GLY* 2.8 28.2 + - - -
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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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46D VAL* 4.0 4.7 - - + -
301D TYR* 5.9 0.7 - - - -
303D ILE* 3.7 31.1 - - + +
308D ASN 2.9 11.0 + - - +
309D MET 3.0 9.8 + - - +
311D ALA* 1.3 76.3 - - - +
313D PHE* 1.3 58.6 + - - +
315D GLY* 3.9 0.8 - - - -
316D MET* 3.0 30.0 + - - +
325D THR* 3.6 11.1 - - + +
327D VAL* 3.6 27.1 - - + -
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Residues in contact with PHE 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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13D PHE* 3.9 8.3 - + - -
17D PRO* 3.8 21.8 - - + -
22D PHE* 3.7 26.7 - + - -
46D VAL* 3.9 18.3 - - + +
47D ASP 3.7 19.5 - - - -
50D MET* 3.7 15.0 - - + -
51D ARG* 3.7 23.6 - - + -
63D MET* 4.6 1.3 - - + -
91D TRP* 3.7 25.4 - + + -
309D MET 3.0 5.6 + - - +
310D PRO 3.4 5.8 - - - +
312D ALA* 1.3 77.8 - - - +
314D MET* 1.3 62.4 + - + +
316D MET* 3.2 16.4 + - + +
317D LEU* 3.1 44.9 + - + +
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Residues in contact with MET 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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18A THR* 3.9 9.0 - - + +
19A ASN* 4.5 2.0 - - - -
20A SER* 5.6 7.2 - - - +
16D TYR* 5.5 0.6 - - + -
17D PRO* 3.1 51.4 - - + +
18D THR* 3.6 9.6 - - - +
19D ASN* 3.2 27.4 - - - +
22D PHE* 3.8 15.7 - - + -
310D PRO* 2.8 37.8 + - + +
311D ALA* 3.8 8.3 - - - +
313D PHE* 1.3 78.3 - - + +
315D GLY* 1.3 61.3 + - - +
317D LEU* 3.3 9.6 + - - +
318D LYS* 3.1 28.8 + - + +
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Residues in contact with GLY 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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20A SER* 5.7 3.6 - - - -
301D TYR* 5.9 1.8 - - - -
311D ALA 2.8 23.0 + - - -
312D ALA* 3.9 1.1 - - - -
314D MET* 1.3 73.1 - - - +
316D MET* 1.3 59.0 + - - +
318D LYS* 3.2 5.6 + - - -
319D GLY 3.0 5.2 + - - -
320D ASP* 2.9 50.7 + - - +
321D ASN* 5.7 0.2 - - - -
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Residues in contact with MET 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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46D VAL* 4.3 4.0 - - + +
47D ASP* 3.5 15.3 - - - +
48D PRO* 3.5 45.8 - - + -
301D TYR* 6.0 0.4 - - - -
312D ALA 3.0 17.7 + - - +
313D PHE* 3.2 21.7 + - + +
315D GLY* 1.3 76.1 - - - +
317D LEU* 1.3 78.7 + - + +
319D GLY 3.1 10.0 + - - -
321D ASN* 3.3 12.3 - - - +
325D THR* 3.5 28.0 - - - +
701D NAP 3.2 39.7 - - - +
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Residues in contact with LEU 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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16D TYR* 3.9 21.7 + - + -
17D PRO* 3.7 30.5 - - + -
48D PRO* 4.2 10.1 - - + -
51D ARG* 4.2 17.9 - - + -
242D ILE* 4.2 15.1 - - + +
245D TYR* 5.3 0.7 - - + -
246D ASN* 4.1 15.1 + - - +
313D PHE* 3.1 41.3 + - + +
314D MET* 3.7 7.9 - - - +
315D GLY 3.2 0.2 - - - -
316D MET* 1.3 98.8 - - + +
318D LYS* 1.3 57.8 + - - +
319D GLY 3.3 0.4 - - - -
701D NAP 3.4 24.4 + - - -
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Residues in contact with LYS 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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12A HIS 5.0 1.4 + - - -
14A VAL* 4.0 23.2 + - - +
16A TYR 5.3 0.2 + - - -
18A THR* 3.5 27.6 - - + -
20A SER* 4.3 14.6 - - - +
21A ASP* 3.8 20.3 + - - +
16D TYR* 3.4 44.1 + - + +
194D LYS* 4.6 10.7 + - - -
314D MET 3.1 19.4 + - - +
315D GLY* 3.2 5.8 + - - +
316D MET 3.1 0.2 - - - -
317D LEU* 1.3 78.5 - - - +
319D GLY* 1.3 59.2 + - - +
320D ASP* 3.5 11.2 + - - +
701D NAP 5.1 2.0 - - - -
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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