Contacts of the helix formed by residues 308 - 318 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ILE* 3.5 17.9 - - + +
304B GLU 2.9 23.4 + - - -
305B GLY* 2.9 13.2 + - - +
307B GLU* 1.3 87.6 - - - +
309B MET* 1.3 56.0 + - - +
310B PRO* 3.5 2.5 - - - -
311B ALA* 3.2 16.4 + - + +
312B ALA* 2.9 27.4 + - - +
140C LYS 4.8 8.5 + - - -
141C GLY* 5.9 0.8 - - - -
165C LYS 5.2 5.5 + - - -
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Residues in contact with MET 309 (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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7B TRP* 3.8 3.6 - - + -
44B LEU* 3.8 37.7 - - + -
45B THR 3.5 22.9 - - - +
46B VAL* 3.9 11.2 - - + +
65B GLY* 6.1 0.2 - - - -
66B GLN 5.7 0.4 - - - +
91B TRP* 3.3 55.4 - - + +
305B GLY 4.0 0.2 + - - -
306B PHE* 3.2 23.4 + - - +
308B ASN* 1.3 74.7 - - - +
310B PRO* 1.3 75.9 - - + +
312B ALA* 2.9 13.2 + - - +
313B PHE* 3.0 13.3 + - - +
327B VAL* 4.0 16.2 - - + -
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Residues in contact with PRO 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TRP* 3.3 51.1 - - + +
19B ASN* 5.3 2.0 - - - +
22B PHE* 3.8 32.3 - - + -
91B TRP* 4.0 11.2 - - + -
307B GLU 4.2 1.3 - - - +
308B ASN 3.7 1.6 - - - -
309B MET* 1.3 94.0 - - + +
311B ALA* 1.3 55.9 - - - +
313B PHE* 3.2 5.6 + - + +
314B MET* 2.8 41.2 + - + +
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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
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19B ASN* 5.7 1.8 - - - +
303B ILE* 5.5 1.6 - - + -
308B ASN* 3.2 22.3 + - + +
309B MET 3.2 0.4 - - - -
310B PRO* 1.3 80.2 - - - +
312B ALA* 1.3 56.7 + - - +
314B MET* 3.8 12.5 - - + +
315B GLY* 2.9 26.9 + - - -
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.8 4.7 - - + -
301B TYR* 5.8 0.7 - - - -
303B ILE* 3.9 28.9 - - + +
308B ASN 2.9 10.0 + - - +
309B MET 2.9 8.3 + - - +
311B ALA* 1.3 75.0 - - - +
313B PHE* 1.3 59.5 + - - +
315B GLY 3.9 0.2 - - - -
316B MET* 3.0 31.0 + - - +
325B THR* 3.7 11.5 - - + +
327B VAL* 3.5 28.7 - - + -
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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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13B PHE* 4.2 8.3 - + - -
17B PRO* 3.7 22.9 - - + -
22B PHE* 3.8 24.7 - + - -
46B VAL* 3.7 17.8 - - + +
47B ASP 3.5 22.2 - - - -
50B MET* 3.8 13.2 - - + -
51B ARG* 3.6 25.4 - - - -
63B MET* 4.6 2.0 - - + -
91B TRP* 3.7 17.9 - + + -
309B MET 3.0 10.4 + - - +
310B PRO 3.4 6.7 - - - +
312B ALA* 1.3 74.2 - - - +
314B MET* 1.3 61.5 + - + +
316B MET* 3.4 13.3 + - + +
317B LEU* 2.9 54.4 + - + +
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Residues in contact with MET 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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16B TYR* 5.3 1.0 - - + -
17B PRO* 3.2 50.5 - - + +
18B THR* 3.6 10.8 - - - -
19B ASN* 3.0 30.1 - - - +
22B PHE* 4.0 8.3 - - + -
310B PRO* 2.8 45.3 + - + +
311B ALA* 3.8 9.0 - - - +
313B PHE* 1.3 71.7 - - - +
315B GLY* 1.3 57.8 + - - +
317B LEU* 3.3 10.6 + - - +
318B LYS* 3.0 32.8 + - + +
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Residues in contact with GLY 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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301B TYR* 5.9 1.6 - - - -
311B ALA 2.9 18.5 + - - -
312B ALA* 3.9 1.1 - - - -
314B MET* 1.3 73.4 - - - +
316B MET* 1.3 56.2 + - - +
318B LYS* 3.2 4.9 + - - -
319B GLY 3.0 8.1 + - - -
320B ASP* 2.7 57.4 + - - +
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Residues in contact with MET 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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46B VAL* 3.9 6.5 - - + +
47B ASP* 3.3 45.5 - - - +
48B PRO* 3.4 22.7 - - + -
301B TYR* 5.9 0.8 - - - -
312B ALA 3.0 19.1 + - - +
313B PHE* 3.6 19.1 - - + +
315B GLY* 1.3 72.0 - - - +
317B LEU* 1.3 73.5 + - + +
319B GLY 3.0 11.1 + - - -
321B ASN* 3.4 11.2 - - - +
325B THR* 3.4 27.0 - - - +
701B NAP 3.3 38.2 - - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 3.7 22.7 + - + -
17B PRO* 3.6 31.6 - - + -
48B PRO* 4.4 9.0 - - + -
51B ARG* 4.2 17.3 - - + -
242B ILE* 4.5 14.5 - - + +
245B TYR* 5.4 0.7 - - + -
246B ASN* 3.9 17.1 + - - +
313B PHE* 2.9 41.5 + - + +
314B MET* 3.3 8.9 + - - +
316B MET* 1.3 93.6 - - + +
318B LYS* 1.3 58.9 + - - +
319B GLY 3.3 0.7 + - - -
701B NAP 3.6 19.8 + - - -
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Residues in contact with LYS 318 (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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16B TYR* 3.5 51.2 + - + +
194B LYS* 4.6 12.1 + - - -
314B MET* 3.0 18.7 + - + +
315B GLY* 3.2 8.0 + - - +
316B MET 3.1 0.6 - - - -
317B LEU* 1.3 76.8 - - - +
319B GLY* 1.3 59.4 + - - +
320B ASP* 3.5 8.9 + - - +
701B NAP 5.1 2.2 - - - -
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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
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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