Contacts of the helix formed by residues 348 - 356 (chain B) in PDB entry 1YSD
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 ARG 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B TYR* 6.0 3.6 - - - -
229B GLY* 2.9 32.3 + - - -
230B GLY* 4.3 2.0 + - - +
254B PHE* 3.4 32.0 - - - -
344B PHE* 2.8 46.5 + - + +
345B ILE 3.8 2.9 - - - -
347B GLU* 1.3 89.5 - - + +
349B PRO* 1.3 65.4 - - - +
350B GLN 3.3 2.7 - - - -
351B ASP* 2.6 39.6 + - + +
352B TRP* 3.1 19.9 + - - +
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Residues in contact with PRO 349 (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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345B ILE* 3.3 14.5 - - + +
346B ASP 3.3 16.4 - - - +
347B GLU 3.5 4.5 - - - +
348B ARG* 1.3 87.6 - - - +
350B GLN* 1.3 72.4 + - + +
352B TRP* 3.3 5.3 + - + +
353B PHE* 2.8 43.3 + - + -
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Residues in contact with GLN 350 (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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75A GLU* 5.0 10.6 - - - +
348B ARG 3.3 1.0 - - - -
349B PRO* 1.3 86.1 - - + +
351B ASP* 1.3 66.1 + - - +
353B PHE* 3.8 13.4 + - - +
354B GLU* 3.3 20.6 + - - +
358B GLU 5.3 2.3 - - - +
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Residues in contact with ASP 351 (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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73A ARG* 5.2 1.0 + - - -
253B ARG* 4.9 0.2 - - - -
254B PHE* 3.4 35.7 - - + -
344B PHE* 4.2 5.9 - - + -
348B ARG* 2.6 53.0 + - + +
350B GLN* 1.3 81.1 - - - +
352B TRP* 1.3 66.0 + - - +
354B GLU* 3.4 10.4 + - - +
355B ASP* 3.2 20.8 + - - +
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Residues in contact with TRP 352 (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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231B VAL* 4.5 1.3 - - + -
233B ILE* 4.0 13.2 - - + -
288B LEU* 3.8 19.5 - - + -
313B ASN 4.6 4.5 + - - -
314B PHE* 3.4 38.5 - + + -
341B MET* 3.5 24.9 - - + -
344B PHE* 3.9 16.0 - + + -
345B ILE* 3.8 33.6 - - + +
348B ARG 3.1 11.1 + - - +
349B PRO* 3.3 10.1 + - + +
351B ASP* 1.3 77.8 - - - +
353B PHE* 1.3 82.6 + + - +
355B ASP* 3.1 26.4 + - + +
356B ILE* 3.4 33.0 + - + +
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Residues in contact with PHE 353 (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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345B ILE* 5.8 2.2 - - + -
349B PRO* 2.8 35.1 + - + +
350B GLN* 4.0 14.1 - - - +
352B TRP* 1.3 100.9 - + - +
354B GLU* 1.3 61.1 + - - +
356B ILE* 3.1 18.3 + - + +
357B GLY 3.2 0.2 + - - -
358B GLU* 2.7 74.9 + - + +
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Residues in contact with GLU 354 (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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73A ARG* 2.7 54.2 + - - +
74A LEU 4.0 19.0 - - - +
75A GLU* 4.9 13.2 - - - +
76A GLY 5.4 3.1 - - - +
101A TYR* 4.4 2.8 - - - -
253B ARG* 3.1 32.1 + - - +
254B PHE* 4.5 5.0 - - - -
350B GLN 3.3 13.5 + - - +
351B ASP* 3.7 12.0 - - - +
352B TRP 3.2 0.4 - - - -
353B PHE* 1.3 79.2 - - - +
355B ASP* 1.3 62.6 + - - +
357B GLY* 3.0 14.0 + - - +
358B GLU 4.3 5.6 + - - +
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Residues in contact with ASP 355 (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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100A MET* 4.0 2.8 - - - +
231B VAL* 4.3 11.5 - - + +
233B ILE* 4.4 4.9 - - - +
251B ASN* 2.9 31.5 + - - -
253B ARG* 2.8 35.1 + - - +
262B HIS* 2.7 48.7 + - - -
351B ASP 3.2 8.9 + - - +
352B TRP* 3.1 31.0 + - + +
354B GLU* 1.3 79.4 - - - +
356B ILE* 1.3 60.7 + - - +
357B GLY 3.4 1.0 + - - -
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Residues in contact with ILE 356 (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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100A MET* 3.7 23.3 - - + +
262B HIS* 5.1 5.6 - - + -
291B CYS* 5.3 3.1 - - + -
314B PHE* 3.9 28.7 - - + -
352B TRP* 3.6 52.0 - - + +
353B PHE* 3.3 18.2 - - + +
355B ASP* 1.3 83.7 - - - +
357B GLY* 1.3 60.8 + - - +
358B GLU* 3.3 30.2 + - + +
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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