Contacts of the helix formed by residues 308 - 318 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303C ILE* 3.7 18.3 - - + +
304C GLU 2.9 21.2 + - - -
305C GLY 3.0 11.0 + - - +
307C GLU* 1.3 96.7 + - - +
309C MET* 1.3 56.6 + - - +
310C PRO* 3.4 3.1 - - - -
311C ALA* 3.2 16.1 + - + +
312C ALA* 3.0 26.0 + - - +
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Residues in contact with MET 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C TRP* 4.0 3.6 - - + -
44C LEU* 3.7 39.3 - - + -
45C THR 3.4 26.0 - - - +
46C VAL* 3.7 7.3 - - + +
65C GLY* 6.2 0.2 - - - -
66C GLN 5.7 0.2 - - - +
91C TRP* 3.6 49.4 - - + +
305C GLY 4.0 0.4 + - - -
306C PHE* 3.2 22.7 + - - +
308C ASN* 1.3 72.9 - - - +
310C PRO* 1.3 74.2 - - + +
312C ALA* 3.2 2.1 + - - +
313C PHE* 3.1 23.4 + - - +
327C VAL* 3.8 21.1 - - + -
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Residues in contact with PRO 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C TRP* 3.4 56.1 - - + +
19C ASN* 5.1 4.7 - - - +
22C PHE* 3.8 29.2 - - + -
91C TRP* 3.9 11.4 - - + -
307C GLU 3.8 2.0 - - - +
308C ASN 3.5 3.8 - - - -
309C MET* 1.3 89.7 - - + +
311C ALA* 1.3 55.4 + - - +
313C PHE* 3.2 5.5 + - + +
314C MET* 3.0 38.9 + - + +
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Residues in contact with ALA 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ASN* 5.1 6.5 - - - +
303C ILE* 6.0 0.9 - - + -
308C ASN* 3.2 20.9 + - + +
310C PRO* 1.3 79.0 - - - +
312C ALA* 1.3 56.4 + - - +
314C MET* 3.8 14.8 - - + +
315C GLY* 3.0 26.2 + - - -
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Residues in contact with ALA 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C VAL* 4.0 4.3 - - + -
301C TYR* 6.0 0.9 - - - -
303C ILE* 4.0 25.8 - - + +
308C ASN 3.0 12.9 + - - +
309C MET 3.2 7.6 + - - +
311C ALA* 1.3 76.5 - - - +
313C PHE* 1.3 58.1 + - - +
315C GLY* 4.0 0.6 - - - -
316C MET* 3.0 30.3 + - - +
325C THR* 3.7 17.4 - - + +
327C VAL* 3.9 21.3 - - + -
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Residues in contact with PHE 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PHE* 4.1 15.9 - + - -
17C PRO* 4.0 21.1 - - + -
22C PHE* 3.9 13.2 - + - -
46C VAL* 3.8 19.2 - - + +
47C ASP 3.6 20.6 - - - -
50C MET* 3.7 11.9 - - + -
51C ARG* 3.6 27.6 - - + -
63C MET* 4.5 1.8 - - + -
91C TRP* 3.7 26.9 - + + -
309C MET 3.1 12.1 + - - +
310C PRO 3.4 6.1 - - - +
312C ALA* 1.3 76.3 - - - +
314C MET* 1.3 64.6 + - - +
316C MET* 3.5 16.4 + - + +
317C LEU* 3.1 39.5 + - + +
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Residues in contact with MET 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C PRO* 3.3 46.4 - - + +
18C THR* 3.6 15.9 - - - -
19C ASN* 3.6 36.3 - - - +
22C PHE* 4.2 5.2 - - + -
310C PRO* 3.0 33.6 + - + +
311C ALA* 3.8 8.1 - - + +
313C PHE* 1.3 75.3 - - - +
315C GLY* 1.3 56.3 + - - +
317C LEU* 3.1 12.0 + - - +
318C LYS* 3.0 42.1 + - + +
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Residues in contact with GLY 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C TYR* 6.0 0.2 - - - -
311C ALA 3.0 17.1 + - - -
312C ALA* 4.1 0.7 - - - -
314C MET* 1.3 72.5 - - - +
316C MET* 1.3 56.5 + - - +
318C LYS* 3.2 7.2 + - - -
319C GLY 2.9 9.7 + - - -
320C ASP* 2.7 56.5 + - - -
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Residues in contact with MET 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C VAL* 4.1 4.0 - - + +
47C ASP* 3.5 40.8 - - - +
48C PRO* 3.5 24.2 - - + -
301C TYR* 5.9 1.2 - - - -
312C ALA 3.0 18.6 + - - +
313C PHE* 3.6 22.7 - - + +
315C GLY* 1.3 74.2 - - - +
317C LEU* 1.3 71.1 + - + +
319C GLY 3.2 8.7 + - - -
320C ASP* 4.5 0.4 - - - +
321C ASN* 3.5 16.4 - - - +
325C THR* 3.4 27.6 - - + +
701C NAP 3.3 29.6 - - - +
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Residues in contact with LEU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C TYR* 3.9 18.9 + - + -
17C PRO* 3.6 36.1 - - + -
48C PRO* 4.3 9.6 - - + -
51C ARG* 4.3 16.4 - - + -
242C ILE* 4.6 11.7 - - + +
245C TYR* 5.4 1.1 - - + -
246C ASN* 3.7 21.7 + - - +
313C PHE* 3.1 27.8 + - + +
314C MET* 3.1 9.7 + - - +
316C MET* 1.3 98.3 - - + +
318C LYS* 1.3 58.1 + - - +
701C NAP 3.3 27.2 + - - -
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Residues in contact with LYS 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C TYR* 3.7 49.9 - - + +
17C PRO 4.6 8.6 + - - -
194C LYS* 4.5 11.4 + - - -
314C MET* 3.0 28.3 + - - +
315C GLY* 3.2 7.8 + - - +
316C MET 3.2 0.6 - - - -
317C LEU* 1.3 77.7 - - - +
319C GLY* 1.3 57.9 + - - -
320C ASP* 3.5 6.9 + - - +
701C NAP 5.1 1.6 - - - -
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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