Contacts of the helix formed by residues 345 - 357 (chain D) in PDB entry 1HH4
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 345 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A THR* 2.5 24.6 + - - -
342D ASP* 3.3 18.4 + - + +
343D LYS 3.3 2.7 - - - -
344D ASP* 1.3 79.1 + - - +
346D GLU* 1.3 68.2 + - - +
347D SER* 2.5 30.3 + - - -
348D LEU* 3.2 31.2 + - + +
349D ARG* 3.2 11.1 + - - +
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Residues in contact with GLU 346 (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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344D ASP 3.4 6.8 + - - +
345D ASP* 1.3 70.8 + - - +
347D SER* 1.3 63.9 + - - +
349D ARG* 2.9 41.0 + - - +
350D LYS* 2.9 60.2 + - - +
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Residues in contact with SER 347 (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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34A PRO* 3.8 14.2 - - - +
35A THR 3.5 5.7 + - - -
36A VAL* 3.2 41.7 + - - +
38A ASP* 5.1 2.7 - - - +
345D ASP* 2.5 23.4 + - - -
346D GLU* 1.3 78.7 - - - +
348D LEU* 1.3 55.4 + - - +
350D LYS* 3.3 14.4 + - - +
351D TYR* 2.9 28.1 + - - +
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Residues in contact with LEU 348 (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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35A THR* 4.0 17.7 - - + -
36A VAL* 3.5 28.7 - - + -
59A ALA* 4.4 9.6 - - + -
61A GLN* 4.9 2.0 - - - +
64A TYR* 3.8 17.9 - - + +
342D ASP* 3.3 37.2 - - + +
345D ASP* 3.2 26.0 + - + +
346D GLU 3.1 0.6 - - - -
347D SER* 1.3 78.1 + - - +
349D ARG* 1.3 57.8 + - - +
351D TYR* 3.1 13.0 + - + +
352D LYS* 2.7 49.0 + - - +
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Residues in contact with ARG 349 (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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342D ASP 5.7 1.1 - - - +
343D LYS* 5.8 6.7 - - - +
345D ASP 3.2 7.7 + - - +
346D GLU* 2.9 42.8 + - - +
348D LEU* 1.3 77.4 - - - +
350D LYS* 1.3 76.0 + - - +
352D LYS* 3.2 13.7 + - + +
353D GLU* 2.8 64.0 + - + +
358D ARG* 5.4 1.8 - - - +
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Residues in contact with LYS 350 (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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38A ASP* 3.0 41.2 + - - +
346D GLU* 2.9 52.4 + - + +
347D SER* 3.6 11.0 - - - +
348D LEU 3.3 0.2 - - - -
349D ARG* 1.3 85.7 - - - +
351D TYR* 1.3 57.3 + - - +
353D GLU* 3.9 7.2 - - - +
354D ALA* 2.9 30.3 + - - +
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Residues in contact with TYR 351 (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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36A VAL* 3.6 23.3 - - + -
38A ASP* 5.0 0.6 + - - -
56A TRP* 5.4 10.5 - + - -
57A ASP 3.4 20.0 - - - -
58A THR* 3.4 30.1 - - + +
59A ALA* 3.5 16.3 + - + -
64A TYR* 5.6 1.3 - + - -
67A LEU* 3.3 24.6 - - + +
68A ARG* 3.8 18.2 + - - +
71A SER* 5.5 1.5 - - - -
347D SER 2.9 13.1 + - - +
348D LEU* 3.1 25.8 - - + +
350D LYS* 1.3 75.5 - - - +
352D LYS* 1.3 67.3 + - + +
354D ALA* 3.5 4.3 + - - +
355D LEU* 3.2 48.4 + - + +
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Residues in contact with LYS 352 (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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64A TYR* 2.6 47.8 + - - -
67A LEU* 4.1 20.9 - - + -
338D ILE* 3.0 22.6 + - + +
339D GLN* 4.3 25.1 + - + +
341D LEU* 3.8 2.1 - - - +
342D ASP 4.5 8.7 - - - -
343D LYS* 6.0 0.4 - - - +
348D LEU* 2.7 44.1 + - - +
349D ARG* 3.7 9.6 - - - +
351D TYR* 1.3 75.4 - - + +
353D GLU* 1.3 60.8 + - - +
355D LEU* 3.3 3.5 + - - -
356D LEU* 2.8 41.7 + - + +
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Residues in contact with GLU 353 (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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339D GLN* 6.3 0.4 - - - +
349D ARG* 2.8 46.7 + - + +
350D LYS* 3.9 7.5 - - - +
352D LYS* 1.3 72.9 - - - +
354D ALA* 1.3 64.6 + - - +
355D LEU 3.0 2.9 + - - -
356D LEU* 5.3 0.2 - - - -
357D GLY* 3.1 35.2 + - - +
358D ARG* 3.6 28.3 + - - +
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Residues in contact with ALA 354 (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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38A ASP* 5.9 1.3 - - - +
39A ASN* 5.4 6.3 - - + +
56A TRP* 4.3 27.5 - - + -
350D LYS 2.9 20.7 + - - +
351D TYR* 3.7 9.0 - - + +
352D LYS 3.4 0.2 - - - -
353D GLU* 1.3 77.3 + - - +
355D LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 355 (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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56A TRP* 4.3 15.0 - - + -
67A LEU* 4.0 28.7 - - + +
68A ARG 4.9 2.9 - - - +
70A LEU* 3.9 20.8 - - + +
71A SER* 4.0 30.5 - - - +
351D TYR* 3.2 49.8 + - + +
352D LYS* 3.9 3.8 - - - +
353D GLU 3.0 0.6 - - - -
354D ALA* 1.3 84.9 - - + +
356D LEU* 1.3 69.8 + - + +
450D GLY* 5.3 2.1 + - - -
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Residues in contact with LEU 356 (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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67A LEU* 4.8 7.0 - - + -
70A LEU* 3.6 31.0 - - + -
335D ILE* 4.0 28.0 - - + -
338D ILE* 4.7 15.3 - - + -
339D GLN* 4.6 13.0 - - + +
352D LYS* 2.8 29.0 + - + +
353D GLU* 5.3 0.2 - - - -
355D LEU* 1.3 79.7 - - + +
357D GLY* 1.3 62.3 + - - +
358D ARG 4.1 0.9 + - - -
422D ILE* 4.5 13.9 - - + -
450D GLY* 4.3 12.7 - - - -
451D PRO* 4.3 21.2 - - + +
452D ARG* 5.7 1.2 - - - +
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Residues in contact with GLY 357 (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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339D GLN* 5.0 7.6 + - - -
352D LYS 4.1 0.4 + - - -
353D GLU* 3.1 27.3 + - - +
356D LEU* 1.3 82.3 - - - +
358D ARG* 1.3 71.2 + - - +
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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