Contacts of the helix formed by residues 306 - 317 (chain A) in PDB entry 3AP1
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 PRO 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A TYR* 3.5 39.7 - - + +
304A HIS 3.8 3.3 - - - +
305A ILE* 1.3 90.7 - - + +
307A GLY* 1.3 65.1 + - - +
308A ASP* 3.5 17.0 - - - +
309A VAL* 3.0 20.7 + - + +
310A VAL* 3.0 9.5 + - - +
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Residues in contact with GLY 307 (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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305A ILE 3.4 3.8 + - - -
306A PRO* 1.3 71.5 - - - +
308A ASP* 1.3 62.3 + - - +
310A VAL* 3.4 9.5 + - - +
311A ARG* 3.1 22.5 + - - +
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Residues in contact with ASP 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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208A ARG* 2.8 26.4 + - - +
306A PRO* 3.5 19.2 - - - +
307A GLY* 1.3 72.9 + - - +
309A VAL* 1.3 61.3 + - - +
311A ARG* 3.4 31.9 - - - +
312A ASP* 3.0 33.4 + - - -
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 4.4 6.1 - - + -
208A ARG* 3.8 33.9 - - + +
211A LEU* 3.6 25.6 - - + -
305A ILE* 3.5 21.1 - - + -
306A PRO* 3.0 20.5 + - + +
308A ASP* 1.3 90.1 - - - +
310A VAL* 1.3 60.0 + - - +
312A ASP 3.1 1.2 + - - -
313A MET* 2.8 33.3 + - + +
316A ILE* 3.9 13.6 - - + +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ILE* 3.6 27.4 - - + +
306A PRO 3.0 14.1 + - - +
307A GLY* 3.5 10.8 - - - +
309A VAL* 1.3 78.3 - - - +
311A ARG* 1.3 63.0 + - - +
313A MET* 3.4 22.2 + - + +
327A PRO 4.7 0.9 - - - +
328A TYR* 4.5 8.1 - - - -
330A ASN* 3.8 34.5 - - - +
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Residues in contact with ARG 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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208A ARG* 4.3 1.0 - - - +
307A GLY 3.1 12.8 + - - +
308A ASP* 3.4 30.5 - - - +
309A VAL 3.2 0.2 - - - -
310A VAL* 1.3 80.2 - - - +
312A ASP* 1.3 90.7 + - - +
313A MET 3.3 0.6 + - - -
315A GLN* 4.5 2.1 + - - -
328A TYR* 3.8 19.3 + - - -
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Residues in contact with ASP 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ARG* 2.9 28.2 + - - +
308A ASP 3.0 13.7 + - - +
309A VAL 3.1 2.0 + - - -
311A ARG* 1.3 109.2 + - - +
313A MET* 1.3 64.9 + - - +
314A ALA 3.2 2.9 - - - -
315A GLN* 2.9 23.1 + - + +
316A ILE* 2.9 35.2 + - + +
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Residues in contact with MET 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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186A ARG* 3.7 26.7 - - + -
211A LEU* 3.7 30.1 - - + -
305A ILE* 4.0 9.4 - - + -
309A VAL* 2.8 28.3 + - + +
310A VAL* 3.4 18.4 + - + +
311A ARG 3.3 2.6 + - - -
312A ASP* 1.3 77.1 - - - +
314A ALA* 1.3 57.2 + - - +
316A ILE* 4.4 4.3 - - - -
317A ALA* 2.9 33.4 + - - +
320A LEU* 3.6 27.4 - - + -
327A PRO* 3.4 25.1 - - + +
328A TYR* 4.8 1.1 - - + -
330A ASN* 6.0 0.7 - - - +
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Residues in contact with ALA 314 (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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312A ASP 3.1 1.0 + - - -
313A MET* 1.3 78.4 - - - +
315A GLN* 1.3 67.5 + - - +
317A ALA 5.0 1.8 - - - -
318A PRO* 3.8 23.3 - - - +
327A PRO* 4.1 21.5 - - + +
328A TYR* 3.5 35.4 - - + +
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Residues in contact with GLN 315 (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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311A ARG 4.5 1.4 + - - -
312A ASP* 2.9 32.1 + - + +
314A ALA* 1.3 83.5 - - - +
316A ILE* 1.3 68.5 + - + +
318A PRO* 3.4 10.2 - - - +
328A TYR* 4.4 12.5 + - - -
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Residues in contact with ILE 316 (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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208A ARG* 3.6 44.6 - - + +
211A LEU* 3.5 32.5 - - + -
212A THR* 3.6 26.9 + - - +
215A ASN* 3.8 11.8 - - - +
309A VAL* 3.9 24.0 - - + +
312A ASP* 2.9 31.3 + - + +
313A MET* 3.9 5.2 - - - +
315A GLN* 1.3 79.1 - - + +
317A ALA* 1.3 58.6 + - + +
318A PRO* 3.4 6.3 - - - +
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Residues in contact with ALA 317 (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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211A LEU* 4.3 8.3 - - + +
214A TRP* 4.1 13.0 - - + -
215A ASN* 3.2 14.1 - - + +
313A MET* 2.9 16.7 + - - +
314A ALA* 4.2 1.8 - - - +
316A ILE* 1.3 83.6 - - + +
318A PRO* 1.4 64.7 - - - +
319A MET 3.1 2.7 - - - -
320A LEU* 3.0 43.1 + - + +
321A ALA 4.4 0.3 + - - -
327A PRO* 5.0 1.0 - - - +
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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