Contacts of the helix formed by residues 361 - 371 (chain A) in PDB entry 3P11
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 ASP 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A SER* 4.6 0.8 + - - -
359A ALA 3.7 2.6 + - - -
360A LEU* 1.3 76.7 - - - +
362A PRO* 1.4 65.5 - - - +
363A GLU* 3.1 32.2 + - - +
364A LYS* 2.7 63.2 + - + +
365A LEU 4.0 0.2 + - - -
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Residues in contact with PRO 362 (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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349A LEU* 6.3 0.2 - - + -
360A LEU* 3.2 12.2 - - + +
361A ASP* 1.4 90.3 - - - +
363A GLU* 1.3 59.9 + - - +
364A LYS 3.2 0.2 - - - -
365A LEU* 3.3 27.5 - - + +
366A ASN* 5.1 0.7 + - - +
384A PRO* 3.7 30.7 - - + -
386A HIS* 3.6 33.7 - - + +
387A MET* 4.1 9.0 - - - +
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Residues in contact with GLU 363 (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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361A ASP* 2.9 29.7 + - - +
362A PRO* 1.3 76.6 - - - +
364A LYS* 1.3 68.3 + - - +
365A LEU 3.1 1.1 - - - -
366A ASN* 2.5 38.0 + - - +
386A HIS* 5.5 0.6 + - - -
387A MET* 6.0 0.2 - - - -
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Residues in contact with LYS 364 (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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326A SER* 5.0 9.2 - - - +
329A ILE* 3.8 33.9 - - + +
330A ASP* 4.2 14.6 + - - +
360A LEU* 4.1 7.0 - - + -
361A ASP* 2.7 43.8 + - + +
363A GLU* 1.3 83.9 - - + +
365A LEU* 1.3 60.3 + - - +
367A VAL* 3.0 25.5 + - - +
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Residues in contact with LEU 365 (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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329A ILE* 4.3 8.6 - - + +
344A PHE* 3.7 32.8 - - + -
349A LEU* 5.2 4.3 - - + -
360A LEU* 5.1 9.8 - - + +
361A ASP 4.0 0.6 + - - +
362A PRO* 3.3 18.5 + - + +
363A GLU 3.1 0.2 - - - -
364A LYS* 1.3 77.7 - - - +
366A ASN* 1.3 63.9 + - - +
367A VAL* 3.1 5.9 - - - +
368A PHE* 2.8 32.7 + - + +
383A TRP* 3.8 26.0 - - + -
384A PRO* 3.6 32.3 - - + -
387A MET* 4.1 8.3 - - + -
392A VAL* 3.5 13.8 - - + +
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Residues in contact with ASN 366 (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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362A PRO 5.3 0.6 - - - +
363A GLU* 2.5 36.2 + - - +
364A LYS 3.1 0.2 + - - -
365A LEU* 1.3 75.1 - - - +
367A VAL* 1.3 53.2 + - - +
368A PHE 2.9 0.2 - - - -
369A ARG* 2.6 62.3 + - - +
370A THR* 5.6 0.7 - - - +
387A MET* 5.0 5.4 - - - +
392A VAL* 3.6 13.9 - - - +
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Residues in contact with VAL 367 (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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329A ILE* 3.7 21.8 - - + +
332A PHE* 3.5 38.6 - - + +
333A VAL* 3.7 17.0 - - + +
334A ASN 4.8 1.5 + - - +
364A LYS 3.0 21.6 + - - +
365A LEU 2.9 6.9 - - - +
366A ASN* 1.3 75.9 - - - +
368A PHE* 1.3 75.7 + - + +
369A ARG 3.3 0.7 + - - -
370A THR* 3.1 26.4 + - - +
371A VAL* 4.8 0.9 - - - +
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Residues in contact with PHE 368 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A VAL* 4.8 2.2 - - + -
329A ILE* 3.6 20.2 - - + -
332A PHE* 4.0 40.8 - + + -
338A ILE* 4.6 0.9 - - + -
342A LEU* 3.6 26.7 - - + -
344A PHE* 3.4 34.3 - + - -
365A LEU* 2.8 28.4 + - + -
366A ASN 2.8 2.6 + - - -
367A VAL* 1.3 74.2 - - + +
369A ARG* 1.3 62.7 + - - +
370A THR 3.1 3.1 - - - -
371A VAL* 3.1 36.6 + - + +
392A VAL* 3.1 19.4 - - + +
393A PHE* 3.4 28.3 - + + -
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Residues in contact with ARG 369 (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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366A ASN* 2.6 49.0 + - - +
368A PHE* 1.3 71.5 - - - +
370A THR* 1.3 60.0 + - + +
371A VAL 3.3 0.2 - - - -
387A MET* 5.5 3.6 - - - +
391A SER* 2.9 47.9 + - - +
392A VAL* 3.2 22.2 + - - +
393A PHE* 5.4 0.2 - - - +
394A SER* 3.6 10.8 + - - +
395A ASN* 3.3 31.9 + - - +
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Residues in contact with THR 370 (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 LEU* 4.9 7.9 - - + +
334A ASN* 3.6 16.5 - - - +
335A CYS 2.8 31.0 + - - +
336A THR* 3.7 12.2 - - - +
366A ASN 5.6 0.2 - - - +
367A VAL* 3.1 18.2 + - - +
369A ARG* 1.3 79.2 - - + +
371A VAL* 1.3 61.7 + - - +
372A ARG* 3.6 4.3 + - - +
395A ASN* 5.0 2.6 - - - +
623A NAG 3.1 41.7 - - + +
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Residues in contact with VAL 371 (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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332A PHE* 6.3 0.7 - - + -
335A CYS* 3.4 16.4 - - + +
336A THR 3.1 13.7 - - - +
338A ILE* 3.8 26.2 - - + -
367A VAL 4.8 0.4 - - - +
368A PHE* 3.1 37.4 + - + +
370A THR* 1.3 79.4 - - - +
372A ARG* 1.3 61.1 + - - +
373A GLU 3.8 15.9 - - - +
374A ILE* 4.3 12.6 - - + -
393A PHE* 4.9 6.9 - - + -
395A ASN* 3.2 8.1 - - - +
396A LEU* 3.2 25.7 + - + -
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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