Contacts of the helix formed by residues 307 - 313 (chain A) in PDB entry 2P80
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 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ARG* 3.2 18.4 - - - +
305A ASN* 2.8 9.5 + - - +
306A HIS* 1.3 73.8 - - - +
308A LEU* 1.3 64.8 + - - +
309A ILE* 3.2 15.1 + - - +
310A GLU* 1.9 84.0 + - + +
311A ALA 2.7 19.4 + - - -
213C LEU* 4.2 9.3 - - - +
249C ASN* 5.2 15.8 + - - -
250C ARG* 5.4 5.7 - - - +
285C GLY 5.3 1.0 - - - -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ILE* 6.4 1.6 - - + -
304A VAL* 5.6 1.8 - - + -
305A ASN 5.0 1.6 - - - +
306A HIS* 1.9 37.8 + - + +
307A ASN* 1.3 67.4 + - - +
309A ILE* 1.3 57.2 + - - +
311A ALA* 3.0 3.7 + - + +
312A PHE* 2.7 45.3 + - + +
135C HIS* 5.2 7.9 - - + +
142C VAL* 3.3 24.7 - - + -
143C PRO* 3.8 14.1 - - + -
146C VAL* 3.0 44.9 - - + -
248C ALA 4.2 5.2 - - - +
249C ASN* 3.0 20.9 + - - +
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ASN* 3.0 8.9 - - - +
308A LEU* 1.3 77.8 - - - +
310A GLU* 1.3 58.6 + - - +
313A GLU* 2.8 41.8 + - + +
314A LEU* 3.1 9.4 + - + -
143C PRO* 4.2 8.3 - - + -
147C VAL* 4.8 0.4 - - + -
184C TYR* 3.7 31.4 - - + +
210C MET* 3.3 58.8 - - + +
211C ARG* 4.3 3.8 - - - -
213C LEU* 3.6 17.9 - - + -
249C ASN* 4.0 15.7 - - - +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL* 4.1 5.6 - - + +
250A ARG* 3.2 31.8 + - - +
253A ARG* 3.1 9.1 + - - -
305A ASN* 2.5 33.1 + - + +
307A ASN* 1.9 72.1 + - + +
309A ILE* 1.3 74.1 - - - +
311A ALA* 1.3 56.6 + - - +
314A LEU* 3.3 19.7 - - + +
315A GLY 3.2 9.7 + - - -
316A ALA* 2.9 25.9 + - + +
213C LEU* 4.2 11.8 - - + +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A VAL* 2.8 40.2 - - + -
305A ASN 3.0 11.9 - - - +
306A HIS 4.6 0.2 - - - +
307A ASN 2.7 12.2 + - - +
308A LEU* 3.7 6.7 - - + +
310A GLU* 1.3 76.4 - - - +
312A PHE* 1.3 67.1 + - + +
315A GLY* 4.3 2.3 + - - -
316A ALA* 3.3 16.0 + - - +
317A ALA* 3.2 21.6 - - + +
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Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ILE* 4.8 18.8 - - + -
302A ALA* 5.7 4.5 - - + -
304A VAL* 5.4 2.5 - - + -
308A LEU* 2.7 29.8 + - + -
311A ALA* 1.3 83.6 - - + +
313A GLU* 1.3 66.0 + - + +
314A LEU 3.6 0.6 - - - -
315A GLY* 4.6 2.8 + - - -
317A ALA* 5.0 9.6 - - + -
319A HIS* 5.9 3.1 - - - -
139C PRO* 6.4 0.2 - - + -
140C GLY* 5.6 10.5 - - - +
142C VAL* 3.3 37.9 - - + -
143C PRO* 3.4 35.0 - - + -
38D LYS* 5.6 6.1 - - - -
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A THR 5.5 0.2 - - - +
309A ILE* 2.8 28.8 + - + +
312A PHE* 1.3 82.7 - - - +
314A LEU* 1.3 60.3 + - + +
143C PRO* 4.3 19.6 - - + +
203C TYR* 4.6 7.4 + - - -
207C VAL* 3.8 29.2 - - + +
210C MET* 5.0 7.9 - - + +
211C ARG* 2.8 54.5 + - + +
9D ASN* 4.8 11.2 + - - +
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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