Contacts of the helix formed by residues 380 - 387 (chain D) in PDB entry 4C3P
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 HIS 380 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355D GLY* 3.4 26.0 - - - -
358D ASP* 2.7 29.6 + - + -
359D LEU* 3.9 25.6 + - + +
362D ARG* 5.0 6.7 - - - -
376D GLU 3.1 18.7 + - - +
377D VAL* 3.3 14.8 + - - +
379D GLU* 1.3 75.0 - - - +
381D PRO* 1.3 84.4 - - + +
382D TRP* 3.2 22.0 + - + +
383D ILE* 2.9 24.6 + - + +
384D THR 3.4 3.1 + - - -
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Residues in contact with PRO 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D GLU 3.3 4.7 - - - +
380D HIS* 1.3 103.5 - - + +
382D TRP* 1.3 57.3 + - - +
384D THR* 3.0 11.7 + - - +
385D ALA* 2.8 32.4 + - - +
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Residues in contact with TRP 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D GLU* 2.8 56.4 + - + -
233D THR* 4.0 13.7 - - + -
234D ALA* 4.0 9.2 - - + -
319D CYS* 4.2 15.3 - - - -
323D LEU* 4.0 20.2 - - + -
353D THR* 3.5 7.7 + - - -
355D GLY* 3.7 12.1 - - - +
356D ALA* 3.7 28.7 - - + +
359D LEU* 3.8 9.4 - - + -
380D HIS* 3.1 23.2 + - + +
381D PRO* 1.3 78.6 - - - +
383D ILE* 1.3 88.7 + - + +
385D ALA* 4.1 3.8 - - - -
386D ASN* 2.7 40.2 + - - +
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Residues in contact with ILE 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ALA* 3.7 9.9 - - - +
237D ILE* 3.9 26.5 - - + -
238D THR* 3.1 28.0 - - + +
359D LEU* 3.7 21.8 - - + -
377D VAL* 3.2 26.7 - - + +
378D LEU* 4.3 11.9 - - + +
380D HIS* 2.9 11.2 + - + +
382D TRP* 1.3 98.7 - - + +
384D THR* 1.3 56.2 + - + +
386D ASN 3.0 3.3 + - - -
387D SER* 2.8 37.3 + - - -
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Residues in contact with THR 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D LEU 3.6 22.4 - - - +
379D GLU* 3.8 17.6 + - - +
380D HIS 3.4 0.2 + - - -
381D PRO* 3.0 20.4 + - - +
383D ILE* 1.3 76.5 - - + +
385D ALA* 1.3 59.8 + - - +
386D ASN 3.5 0.5 + - - -
387D SER* 4.5 8.7 + - - +
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Residues in contact with ALA 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D PRO 2.8 20.7 + - - +
382D TRP* 3.6 9.0 - - + +
383D ILE 3.1 0.2 - - - -
384D THR* 1.3 78.0 + - - +
386D ASN* 1.3 70.8 + - - +
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Residues in contact with ASN 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D GLU* 3.5 44.7 + - - +
231D GLN* 3.0 29.5 + - - +
234D ALA* 3.8 5.2 - - + -
382D TRP* 2.7 47.2 + - + +
383D ILE 3.0 2.0 + - - -
385D ALA* 1.3 91.8 - - - +
387D SER* 1.3 67.2 + - - +
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Residues in contact with SER 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ALA* 3.7 7.3 - - - +
235D THR* 3.3 21.9 - - - -
238D THR* 3.5 15.7 + - - -
383D ILE* 2.8 22.6 + - - -
384D THR* 4.5 7.9 + - - +
386D ASN* 1.3 73.0 - - - +
388D SER* 1.3 61.3 + - - +
389D LYS* 2.5 31.1 + - - -
390D PRO* 5.3 1.3 - - - -
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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