Contacts of the helix formed by residues 317 - 328 (chain B) in PDB entry 4H1S
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 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B ALA* 3.2 17.9 + - - +
65B PHE* 3.4 35.7 - - + -
66B THR* 3.0 15.4 + - - +
69B GLN* 4.4 7.4 + - - +
316B GLU* 1.3 67.6 - - - +
318B PRO* 1.3 70.3 - - - +
319B SER* 3.2 13.1 + - - -
320B ILE* 3.1 32.1 + - + +
321B LYS* 2.9 30.0 + - - +
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Residues in contact with PRO 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B GLU 3.1 9.6 - - - +
317B ASP* 1.3 91.0 - - - +
319B SER* 1.3 57.8 + - - +
321B LYS* 3.7 6.5 - - + +
322B ALA* 3.1 28.6 + - - +
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ASP* 3.2 11.5 + - - -
318B PRO* 1.3 79.0 - - - +
320B ILE* 1.3 67.2 + - - +
322B ALA* 3.4 5.7 + - - +
323B ASP* 3.2 21.8 + - - +
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Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B VAL* 3.8 18.4 - - + -
62B ALA* 3.6 31.2 - - + +
65B PHE* 3.7 35.7 - - + -
104B PHE* 4.2 11.4 - - + -
107B ALA* 4.0 25.1 - - + -
108B LEU* 4.3 2.9 - - + -
317B ASP* 3.1 18.6 + - - +
319B SER* 1.3 75.5 - - - +
321B LYS* 1.3 53.8 + - - +
323B ASP* 3.0 8.2 + - + +
324B ILE* 2.8 34.0 + - + +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 5.2 8.3 + - - +
43B GLN* 5.1 6.7 - - - +
62B ALA* 3.9 8.8 - - + +
316B GLU* 3.1 44.7 + - + +
317B ASP 2.9 18.4 + - - +
318B PRO* 3.7 8.7 - - + +
320B ILE* 1.3 75.9 - - - +
322B ALA* 1.3 52.8 + - - +
324B ILE* 3.3 16.1 + - + +
325B ASN* 2.7 75.4 + - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B PRO 3.1 19.3 + - - +
319B SER* 3.7 7.4 - - - +
320B ILE 3.2 0.2 - - - -
321B LYS* 1.3 73.8 - - - +
323B ASP* 1.3 60.9 + - - +
325B ASN* 3.6 8.5 + - - +
326B LYS* 3.1 25.8 + - - +
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B HIS* 2.4 35.2 + - - -
104B PHE* 3.6 9.8 - - + -
319B SER 3.2 12.3 + - - +
320B ILE* 3.0 12.6 + - + +
322B ALA* 1.3 75.0 - - - +
324B ILE* 1.3 63.5 + - - +
326B LYS* 3.2 17.2 + - - +
327B TRP* 3.0 52.8 + - - -
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Residues in contact with ILE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.0 16.8 - - + +
42B GLU* 4.0 17.7 - - + +
61B VAL* 3.7 26.2 - - + -
62B ALA* 5.3 2.9 - - + -
92B TRP* 3.4 24.9 - - + -
104B PHE* 3.5 29.1 - - + -
320B ILE* 2.8 23.0 + - + +
321B LYS* 3.5 20.4 - - + +
323B ASP* 1.3 73.0 - - - +
325B ASN* 1.3 64.5 + - - +
326B LYS 3.2 0.2 + - - -
327B TRP 3.3 1.2 + - - -
328B ARG* 2.9 28.0 + - + +
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Residues in contact with ASN 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 5.7 0.7 - - - +
321B LYS* 2.7 60.6 + - - +
322B ALA* 3.9 8.5 - - - +
324B ILE* 1.3 74.1 - - - +
326B LYS* 1.3 62.6 + - - +
328B ARG* 3.6 15.6 + - - +
329B ILE* 3.5 19.9 - - - +
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B ALA 3.1 14.9 + - - +
323B ASP* 3.4 25.2 + - - +
324B ILE 3.2 0.2 - - - -
325B ASN* 1.3 73.7 - - - +
327B TRP* 1.3 76.6 + - + +
329B ILE* 3.2 25.5 + - + +
330B LYS 4.7 0.2 + - - -
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Residues in contact with TRP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B TRP* 3.5 21.8 - + + -
96B TYR* 2.4 65.9 + + - +
99B ALA* 4.0 9.9 - - + -
100B GLU* 3.7 27.8 - - + -
103B HIS* 3.4 43.8 + + + -
104B PHE* 4.1 6.1 - + - -
323B ASP* 3.0 47.4 + - - -
324B ILE 3.9 1.1 - - - +
326B LYS* 1.3 92.8 - - - +
328B ARG* 1.3 61.7 + - - +
329B ILE 3.1 1.2 + - - -
330B LYS* 3.5 4.9 + - - +
331B LEU* 4.1 1.0 - - - +
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Residues in contact with ARG 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 2.9 36.5 + - - +
50B LYS* 3.2 13.2 - - - +
91B ILE* 4.3 5.3 - - - +
92B TRP* 3.8 14.8 - - + +
324B ILE* 2.9 19.9 + - + +
325B ASN* 3.7 14.1 - - - +
326B LYS 3.1 0.6 - - - -
327B TRP* 1.3 73.9 - - - +
329B ILE* 1.3 67.0 + - + +
330B LYS 3.3 0.2 - - - -
331B LEU* 2.9 39.5 + - - +
332B ASP* 3.2 34.4 + - - +
335B SER 4.3 5.5 + - - -
409B GLU* 2.8 43.8 + - - -
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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