Contacts of the helix formed by residues 390 - 402 (chain A) in PDB entry 2GC5
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 SER 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A VAL* 3.4 13.6 - - - +
366A PRO* 4.2 9.0 - - - -
388A LYS* 3.2 2.5 - - - +
389A ASP* 1.3 80.6 - - - +
391A TRP* 1.3 64.1 + - - +
392A GLN* 3.4 19.6 + - - +
393A GLU* 3.4 21.8 + - - +
394A ALA* 3.2 16.6 + - - +
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Residues in contact with TRP 391 (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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339A ILE* 4.1 12.0 - - + +
365A VAL* 3.9 18.4 - - + +
366A PRO 5.2 1.7 + - - -
368A PRO* 4.1 18.4 - - + +
390A SER* 1.3 72.4 - - - +
392A GLN* 1.3 103.2 + - + +
394A ALA* 3.2 1.9 + - - +
395A LEU* 2.8 57.6 + - + +
409A ILE* 4.7 6.3 - - + -
415A LEU* 3.6 31.9 - - + -
418A ALA* 4.1 6.8 - - - +
419A VAL* 3.5 39.5 - - + +
422A THR* 3.6 40.4 - - + -
423A LEU* 4.4 8.7 - - + -
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Residues in contact with GLN 392 (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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390A SER* 3.4 19.7 + - - +
391A TRP* 1.3 132.4 + - + +
393A GLU* 1.3 56.8 + - - +
395A LEU* 3.8 4.1 - - - +
396A ALA* 2.8 30.5 + - - +
422A THR* 5.1 5.6 + - + +
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LYS* 4.5 13.5 + - + +
389A ASP* 4.9 6.3 - - + +
390A SER* 3.4 21.9 + - - +
391A TRP 3.3 0.4 - - - -
392A GLN* 1.3 75.9 - - - +
394A ALA* 1.3 61.0 + - - +
396A ALA* 3.8 6.2 - - - +
397A ALA* 2.9 30.2 + - - +
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Residues in contact with ALA 394 (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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339A ILE* 3.7 12.3 - - + -
363A TYR* 3.6 35.9 - - + -
365A VAL* 3.9 11.0 - - + -
388A LYS* 4.1 12.0 - - + +
390A SER 3.2 12.3 + - - +
391A TRP 3.7 6.5 - - - +
393A GLU* 1.3 77.9 - - - +
395A LEU* 1.3 57.8 + - - +
397A ALA* 3.4 3.3 + - - +
398A SER* 3.0 28.6 + - - -
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Residues in contact with LEU 395 (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 ILE* 4.2 13.2 - - + -
339A ILE* 3.5 10.0 - - + +
391A TRP* 2.8 47.1 + - + +
392A GLN* 3.8 5.2 - - - +
394A ALA* 1.3 70.5 - - - +
396A ALA* 1.3 59.8 + - - +
398A SER* 3.4 3.0 + - - -
399A LEU* 3.0 46.4 + - + +
407A ILE* 3.5 38.6 - - + -
409A ILE* 4.7 6.1 - - + -
423A LEU* 4.5 19.1 - - + -
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Residues in contact with ALA 396 (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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392A GLN 2.8 19.0 + - - +
393A GLU* 3.8 7.4 - - - +
395A LEU* 1.3 74.5 - - - +
397A ALA* 1.3 58.5 + - - +
399A LEU* 3.5 6.1 + - - +
400A ASN* 3.0 31.6 + - - +
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Residues in contact with ALA 397 (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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363A TYR* 4.2 16.6 - - + +
388A LYS* 4.3 17.9 - - - +
393A GLU 2.9 19.5 + - - +
394A ALA* 3.5 7.9 - - - +
395A LEU 3.3 0.2 - - - -
396A ALA* 1.3 75.0 - - - +
398A SER* 1.3 62.7 + - - +
400A ASN* 3.3 5.8 + - - +
401A ASP* 3.0 34.3 + - - +
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Residues in contact with SER 398 (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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337A THR* 2.8 41.7 + - - -
363A TYR* 4.4 6.8 - - - -
394A ALA 3.0 17.8 + - - -
395A LEU* 3.4 4.2 + - - -
397A ALA* 1.3 75.7 - - - +
399A LEU* 1.3 58.0 + - - +
401A ASP* 4.7 3.1 - - - -
402A VAL* 2.9 41.7 + - - +
405A GLN 4.7 2.3 + - - -
407A ILE* 3.7 15.7 - - - +
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Residues in contact with LEU 399 (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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308A PRO* 3.6 36.1 - - + -
310A ILE* 4.9 2.9 - - + -
395A LEU* 3.0 42.0 + - + +
396A ALA* 4.1 4.9 - - - +
398A SER* 1.3 73.7 - - - +
400A ASN* 1.3 65.8 + - - +
403A PRO* 3.3 38.8 - - + +
405A GLN 5.1 0.7 - - - +
407A ILE* 3.4 24.7 - - + -
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Residues in contact with ASN 400 (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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396A ALA 3.0 18.8 + - - +
397A ALA* 3.6 5.6 - - - +
399A LEU* 1.3 78.5 - - - +
401A ASP* 1.3 83.3 + - - +
403A PRO* 4.0 7.3 - - - +
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Residues in contact with ASP 401 (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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363A TYR* 4.4 10.0 + - - -
397A ALA* 3.0 25.4 + - - +
398A SER* 4.0 2.4 - - - +
400A ASN* 1.3 99.2 + - - +
402A VAL* 1.3 74.2 + - + +
403A PRO* 3.7 4.1 - - - +
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Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A THR* 4.8 0.2 - - - +
398A SER* 2.9 22.6 + - - +
399A LEU* 4.6 0.5 - - - +
401A ASP* 1.3 88.4 - - + +
403A PRO* 1.3 66.1 - - - +
404A ASP 3.2 2.5 - - - -
405A GLN* 3.0 54.0 + - + +
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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