Contacts of the helix formed by residues 311 - 322 (chain A) in PDB entry 5DP0
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 THR 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A SER 4.8 3.8 - - - +
310A LEU* 1.3 77.9 - - - +
312A ALA* 1.3 59.4 + - - +
313A ASP* 3.6 6.3 + - - +
314A GLN* 3.0 28.1 + - + +
315A MET* 3.0 25.6 + - - +
481A LYS* 4.9 4.1 - - - +
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Residues in contact with ALA 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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311A THR* 1.3 72.2 - - - +
313A ASP* 1.3 67.9 + - - +
315A MET* 3.1 8.7 + - - +
316A VAL* 3.0 26.0 + - - +
481A LYS* 5.4 2.8 - - - +
484A ASP* 5.5 1.1 - - + -
485A THR* 3.6 14.4 - - - +
488A HIS* 3.3 45.1 - - + +
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Residues in contact with ASP 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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311A THR* 3.4 5.5 + - - +
312A ALA* 1.3 78.0 - - - +
314A GLN* 1.3 64.0 + - - +
316A VAL* 3.2 10.9 + - - +
317A SER* 3.1 25.5 + - - -
488A HIS* 3.2 26.7 + - - -
489A LEU* 5.8 1.2 - - - +
492A LYS* 3.3 21.7 + - - -
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Residues in contact with GLN 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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310A LEU* 4.2 19.6 - - + +
311A THR* 3.0 33.2 + - + +
313A ASP* 1.3 76.8 - - - +
315A MET* 1.3 60.1 + - - +
317A SER* 3.5 7.3 + - - -
318A ALA* 3.3 24.1 + - - +
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Residues in contact with MET 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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307A ALA* 4.0 15.5 - - + +
310A LEU* 4.4 10.1 - - + -
311A THR 3.0 14.5 + - - +
312A ALA 3.1 9.8 + - - +
314A GLN* 1.3 76.0 - - - +
316A VAL* 1.3 65.6 + - - +
318A ALA* 3.5 3.0 + - - +
319A LEU* 3.2 40.0 + - + +
365A PRO* 3.9 31.6 - - + +
478A VAL* 5.6 1.8 - - + -
481A LYS* 3.7 31.0 - - + -
482A ILE* 4.8 17.0 - - + -
485A THR* 3.4 25.8 - - + +
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Residues in contact with VAL 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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312A ALA 3.0 18.6 + - - +
313A ASP* 3.6 14.4 - - - +
315A MET* 1.3 76.5 - - - +
317A SER* 1.3 59.9 + - - +
319A LEU* 3.0 10.3 + - - +
320A LEU* 2.9 40.1 + - + +
443A GLU* 3.6 28.9 - - + +
446A VAL* 4.8 2.1 - - + +
447A CYS* 5.3 2.0 - - - -
485A THR* 3.6 18.8 - - + -
488A HIS* 5.6 1.1 - - - +
489A LEU* 4.0 24.0 - - + -
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Residues in contact with SER 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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313A ASP 3.1 10.3 + - - -
314A GLN* 3.5 12.0 + - - -
316A VAL* 1.3 82.6 - - - +
318A ALA* 1.3 59.6 + - - +
320A LEU* 3.8 9.8 - - - +
321A ASP* 2.9 32.4 + - - +
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Residues in contact with ALA 318 (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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310A LEU* 4.9 5.2 - - + -
314A GLN 3.3 16.7 + - - +
315A MET* 3.7 5.2 - - - +
316A VAL 3.2 0.4 - - - -
317A SER* 1.3 81.2 + - - +
319A LEU* 1.3 61.3 + - - +
321A ASP* 3.6 5.8 + - - +
322A ALA* 3.3 21.7 + - - +
363A ARG* 4.4 6.4 + - - +
365A PRO* 4.4 18.4 - - + -
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Residues in contact with LEU 319 (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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315A MET* 3.2 33.6 + - + +
316A VAL* 3.0 8.6 + - - +
318A ALA* 1.3 76.0 - - - +
320A LEU* 1.3 66.4 + - - +
321A ASP 3.2 0.2 - - - -
322A ALA* 3.1 15.2 + - + +
323A GLU* 3.4 13.9 + - - +
360A TRP* 4.9 6.5 + - - +
363A ARG 4.9 0.7 - - - +
364A VAL* 4.5 11.2 - - + -
365A PRO* 3.7 25.8 - - + -
446A VAL* 3.8 34.4 - - + +
447A CYS* 4.3 17.7 - - - -
450A SER* 4.2 24.2 - - - +
482A ILE* 5.3 3.6 - - + -
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Residues in contact with LEU 320 (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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316A VAL* 2.9 39.6 + - + +
317A SER* 3.8 8.3 - - - +
319A LEU* 1.3 75.7 - - - +
321A ASP* 1.3 63.3 + - - +
323A GLU* 3.4 24.4 + - + +
442A GLY* 4.3 14.4 - - - +
443A GLU* 4.2 15.7 - - + +
446A VAL* 4.1 23.6 - - + -
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Residues in contact with ASP 321 (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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317A SER 2.9 19.3 + - - +
318A ALA* 3.9 7.0 - - - +
319A LEU 3.2 0.2 - - - -
320A LEU* 1.3 76.9 - - - +
322A ALA* 1.3 59.4 + - - +
323A GLU 3.2 4.5 + - - +
363A ARG* 2.7 31.3 + - - +
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Residues in contact with ALA 322 (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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318A ALA 3.3 14.3 + - - +
319A LEU* 3.1 9.9 + - + +
321A ASP* 1.3 77.7 - - - +
323A GLU* 1.3 66.1 + - - +
324A PRO* 3.3 1.4 - - - +
360A TRP* 3.2 33.0 - - + +
363A ARG* 3.6 47.3 + - + +
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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