Contacts of the helix formed by residues 388 - 395 (chain A) in PDB entry 4WTM
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 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A ARG 3.3 7.2 - - - +
387A ASP* 1.3 92.2 - - - +
389A THR* 1.3 56.6 + - - +
390A THR 3.4 0.9 - - - -
391A PRO* 3.3 11.3 - - + +
392A LEU* 2.8 42.4 + - + +
420A TRP* 3.6 40.6 - - + -
484A ARG* 4.2 11.4 - - + +
485A VAL* 4.3 15.9 - - + +
488A ALA* 3.7 19.3 - - + -
489A LEU* 6.3 0.4 - - + -
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Residues in contact with THR 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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146A CYS* 3.7 23.6 - - + +
387A ASP* 2.6 27.3 + - - -
388A PRO* 1.3 78.2 - - - +
390A THR* 1.3 64.9 + - - +
392A LEU* 3.2 2.8 + - - +
393A ALA* 3.0 27.0 + - - +
488A ALA* 3.6 8.9 - - - +
491A LYS* 2.8 42.6 + - - +
492A LEU* 3.8 10.7 - - + +
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Residues in contact with THR 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL 4.1 6.3 - - - +
145A PHE* 4.2 17.3 - - + -
146A CYS 5.2 2.3 + - - +
386A ARG* 3.9 12.0 + - - +
387A ASP 4.5 0.8 + - - -
389A THR* 1.3 78.7 - - - +
391A PRO* 1.3 76.0 - - + +
393A ALA* 3.3 6.0 + - - +
394A ARG* 3.0 60.7 + - - +
1P C 4.4 7.2 - - - +
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Residues in contact with PRO 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 3.7 28.9 - - - +
387A ASP 3.6 7.6 - - - +
388A PRO* 3.3 14.6 - - + +
390A THR* 1.3 95.1 - - + +
392A LEU* 1.3 56.1 + - - +
394A ARG* 3.4 6.2 + - + +
395A ALA* 2.9 28.8 + - - +
407A SER* 4.5 0.7 + - - -
411A ASN* 3.6 32.5 - - - +
420A TRP* 3.9 21.1 - - + -
425A LEU* 5.1 4.7 - - + +
1P C 5.7 0.2 - - - +
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Residues in contact with LEU 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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30A LEU* 4.4 17.3 - - + -
31A LEU* 3.6 17.6 - - + +
388A PRO* 2.8 38.7 + - + +
389A THR 3.5 4.3 - - - +
391A PRO* 1.3 70.0 - - + +
393A ALA* 1.3 65.7 + - - +
395A ALA* 3.2 13.2 + - - +
396A ALA 3.4 7.6 + - - -
420A TRP* 5.8 3.4 - - + -
424A VAL* 4.4 22.7 - - + -
425A LEU* 4.4 14.4 - - + -
488A ALA* 4.5 11.4 - - + +
489A LEU* 3.9 24.2 - - + -
492A LEU* 3.7 23.3 - - + -
494A ALA* 5.6 2.2 - - + -
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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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37A VAL* 3.4 35.4 - - + +
144A VAL* 3.9 3.9 - - + +
145A PHE* 3.9 8.3 - - - +
146A CYS* 3.9 28.3 - - + +
389A THR 3.0 16.0 + - - +
390A THR* 3.3 5.8 + - - +
392A LEU* 1.3 76.5 - - - +
394A ARG* 1.3 58.8 + - + +
396A ALA* 3.0 14.7 + - - -
397A TRP 3.4 7.4 + - - -
492A LEU* 4.5 3.1 - - + +
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Residues in contact with ARG 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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143A GLU* 3.8 15.1 + - - -
144A VAL* 2.8 50.2 + - + +
145A PHE* 3.5 26.9 - - - -
390A THR* 3.0 25.8 + - - +
391A PRO* 3.9 4.9 - - + +
393A ALA* 1.3 71.8 - - - +
395A ALA* 1.3 61.8 + - - +
396A ALA 3.0 5.9 + - - -
397A TRP* 3.3 14.3 + - + +
402A HIS* 5.1 1.7 + - - -
404A PRO* 3.8 9.4 - - - +
407A SER* 3.7 21.9 + - - +
1P C 3.1 36.8 + - - -
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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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27A SER* 3.6 11.8 - - - -
30A LEU* 3.6 18.5 - - + +
391A PRO 2.9 17.7 + - - +
392A LEU* 3.4 11.0 - - - +
393A ALA 3.1 0.4 - - - -
394A ARG* 1.3 76.7 - - - +
396A ALA* 1.3 55.8 + - - +
397A TRP 3.6 0.4 - - - -
404A PRO* 3.4 7.4 - - - +
407A SER* 4.0 2.6 + - - +
408A TRP* 2.8 46.5 + - + +
425A LEU* 4.3 9.0 - - + -
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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