Contacts of the helix formed by residues 388 - 398 (chain A) in PDB entry 1A7A
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 LYS 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A VAL* 4.2 10.3 - - - +
386A LEU 3.6 2.6 + - - -
387A PRO* 1.3 71.0 - - - +
389A LYS* 1.3 57.6 + - - +
391A ASP* 3.1 10.4 + - + +
392A GLU* 2.8 54.8 + - + +
424A PRO* 4.4 12.1 - - + -
426A LYS 3.2 31.6 - - - +
427A PRO 3.6 16.2 + - - -
428A ASP* 4.3 17.8 + - - +
430A TYR 5.1 0.2 + - - -
432A TYR* 2.8 40.4 + - - +
247B ILE* 5.5 0.2 - - + -
431B ARG* 4.7 5.5 - - - +
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Residues in contact with LYS 389 (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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387A PRO* 3.0 6.5 + - + +
388A LYS* 1.3 79.3 - - - +
390A LEU* 1.3 63.9 + - + +
392A GLU* 3.5 11.9 + - - +
393A ALA* 3.1 20.3 + - - +
420A SER* 4.9 0.6 + - - -
422A ASP* 3.7 16.3 - - - +
423A GLY* 3.1 38.7 - - - +
424A PRO* 4.0 21.3 - - + +
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Residues in contact with LEU 390 (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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38A ARG* 6.0 5.4 - - - +
367A MSE 3.9 25.2 - - + +
371A GLU* 4.6 19.1 - - + +
386A LEU* 4.5 11.4 - - + -
387A PRO* 2.9 40.2 + - + +
389A LYS* 1.3 77.9 - - + +
391A ASP* 1.3 67.8 + - - +
393A ALA* 3.1 11.7 + - + +
394A VAL* 3.0 25.7 + - - +
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Residues in contact with ASP 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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183A SER* 3.4 14.8 + - - +
184A VAL* 2.6 41.2 + - - +
185A THR* 2.6 43.6 + - - +
364A ASN* 4.7 2.5 - - - -
386A LEU* 5.3 5.0 - - + +
387A PRO 3.0 11.5 + - - +
388A LYS* 3.3 15.3 + - + +
390A LEU* 1.3 77.2 - - - +
392A GLU* 1.3 62.7 + - - +
394A VAL* 3.2 21.4 + - - +
247B ILE* 4.4 3.4 - - + -
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Residues in contact with GLU 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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388A LYS* 2.8 35.4 + - + +
389A LYS* 3.8 9.4 - - + +
391A ASP* 1.3 75.7 - - - +
393A ALA* 1.3 63.4 + - - +
395A ALA* 3.1 5.0 + - - +
396A GLU* 2.8 21.1 + - - +
422A ASP 4.1 3.3 - - - +
423A GLY 3.9 2.1 - - - +
424A PRO* 3.8 14.0 - - - +
425A PHE* 2.9 57.7 + - - +
426A LYS 4.3 0.2 + - - -
432A TYR* 4.6 1.6 + - - -
245B ASP* 4.0 7.5 - - - +
246B PRO* 3.5 16.5 - - + +
247B ILE* 4.0 19.3 - - + -
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Residues in contact with ALA 393 (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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38A ARG* 6.2 2.0 - - - +
367A MSE 4.5 9.4 - - + -
389A LYS 3.1 12.6 + - - +
390A LEU* 3.1 18.3 + - + +
392A GLU* 1.3 79.4 - - - +
394A VAL* 1.3 63.9 + - - +
396A GLU* 2.9 12.5 + - - +
397A ALA* 2.9 24.9 + - - +
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Residues in contact with VAL 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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185A THR* 3.5 18.6 - - - +
360A ASN* 3.9 23.3 - - - +
363A THR* 3.9 12.3 - - + -
364A ASN* 3.5 32.5 - - - +
367A MSE 3.4 30.7 - - + +
390A LEU 3.0 14.6 + - - +
391A ASP 3.3 8.5 - - - +
393A ALA* 1.3 76.2 - - - +
395A ALA* 1.3 62.2 + - - +
397A ALA* 3.2 9.7 + - - +
398A HIS* 2.8 25.3 + - + -
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Residues in contact with ALA 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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185A THR* 3.5 22.2 - - + -
391A ASP 3.4 1.2 + - - -
392A GLU 3.1 9.3 + - - +
394A VAL* 1.3 78.5 - - - +
396A GLU* 1.3 65.1 + - - +
398A HIS* 3.0 12.2 + - - +
399A LEU* 3.0 19.0 - - - +
246B PRO 3.8 2.9 - - - +
247B ILE* 3.7 30.1 - - + +
250B LEU* 4.1 17.2 - - + +
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Residues in contact with GLU 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 GLU* 2.8 17.9 + - - +
393A ALA* 2.9 13.2 + - - +
395A ALA* 1.3 72.8 - - - +
397A ALA* 1.3 62.5 + - - +
398A HIS 3.0 1.7 + - - -
399A LEU* 3.0 28.4 + - + +
400A GLY 4.3 1.4 + - - -
406A LEU* 4.5 9.8 - - + +
408A LYS* 6.1 1.4 - - - -
425A PHE* 6.0 0.3 - - - -
246B PRO* 3.5 26.1 - - + +
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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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30A PRO* 3.8 18.7 - - - +
31A GLY* 4.5 9.9 - - - -
34A ARG* 4.8 18.1 - - + +
363A THR* 5.8 2.2 - - + -
393A ALA 2.9 11.4 + - - +
394A VAL* 3.3 15.5 - - - +
395A ALA 3.1 0.4 - - - -
396A GLU* 1.3 76.7 - - - +
398A HIS* 1.3 65.5 + - + +
399A LEU 3.9 0.2 + - - -
400A GLY 4.8 3.4 + - - -
401A LYS 5.3 0.9 + - - -
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Residues in contact with HIS 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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30A PRO* 3.4 25.6 - - + -
31A GLY* 3.4 19.3 + - - -
356A PHE* 3.6 24.5 - + + -
359A SER* 2.6 33.2 + - - -
360A ASN* 3.4 30.2 + - - +
363A THR* 4.1 8.1 - - - -
394A VAL* 2.8 29.9 + - + -
395A ALA 3.0 7.7 + - - +
397A ALA* 1.3 78.3 - - + +
399A LEU* 1.3 65.9 + - - +
400A GLY 3.4 1.3 - - - -
401A LYS* 3.8 2.8 + - - +
402A LEU* 3.6 25.5 + - - +
250B LEU* 4.6 7.4 - - + -
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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