Contacts of the strand formed by residues 325 - 331 (chain D) in PDB entry 4HYY
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 GLU 325 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107D GLU* 4.7 2.3 - - - +
110D LYS* 4.7 5.2 + - - -
111D LEU* 4.7 1.6 - - - -
304D ARG* 3.6 15.6 + - - -
312D ILE* 3.1 28.0 - - + +
313D ALA 3.2 5.4 - - - +
314D LYS* 3.5 38.2 + - + +
320D GLU 5.2 2.3 - - - +
322D PRO* 3.1 28.8 + - + +
323D GLU 3.3 2.6 - - - +
324D ASN* 1.3 77.6 - - - +
326D ALA* 1.3 61.7 + - - +
327D THR* 5.3 1.1 + - - -
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Residues in contact with ALA 326 (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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107D GLU* 3.4 42.8 - - + +
108D PHE* 4.0 8.3 - - - +
110D LYS* 4.7 2.0 - - + -
111D LEU* 4.2 14.7 - - + +
311D ARG 3.5 4.9 - - - +
312D ILE* 3.6 4.3 - - - +
313D ALA* 3.1 32.5 + - + +
325D GLU* 1.3 75.3 - - - +
327D THR* 1.3 64.4 + - - +
328D PHE* 3.9 2.6 + - + -
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Residues in contact with THR 327 (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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105D SER* 4.4 0.9 + - - -
107D GLU* 3.6 27.7 + - - +
310D LEU* 4.6 16.6 - - + -
311D ARG 3.6 9.2 - - - +
312D ILE* 3.6 16.5 - - + +
325D GLU 5.3 0.9 + - - -
326D ALA* 1.3 74.3 - - - +
328D PHE* 1.3 64.6 + - - +
337D ASP* 4.7 1.6 - - - +
338D ALA* 3.8 32.0 + - + +
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Residues in contact with PHE 328 (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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105D SER* 3.7 18.8 - - - +
108D PHE* 4.1 23.8 - + + -
131D GLY* 4.7 7.2 - - - -
135D LEU* 6.1 0.9 - - + -
303D LEU* 4.0 28.0 - - + -
310D LEU* 3.8 2.4 - - - -
311D ARG* 3.0 64.0 + - + +
312D ILE 4.1 3.4 - - - -
313D ALA* 4.2 2.2 - - + -
326D ALA* 4.4 6.3 - - + -
327D THR* 1.3 78.5 - - - +
329D ALA* 1.3 65.6 + - - +
330D ILE* 3.7 17.3 - - + -
335D ILE* 3.5 34.1 - - + -
336D GLY 3.2 15.3 - - - +
338D ALA* 4.3 4.2 - - - +
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Residues in contact with ALA 329 (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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309D GLU* 3.4 32.8 - - - +
310D LEU* 4.7 4.0 - - - -
311D ARG 4.7 0.2 - - - +
328D PHE* 1.3 80.8 - - - +
330D ILE* 1.3 65.4 + - - +
331D THR* 4.2 4.8 + - + -
335D ILE* 3.7 0.7 - - - -
336D GLY* 3.0 32.4 + - - +
337D ASP 4.1 14.1 - - - +
338D ALA* 4.1 9.3 - - - +
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Residues in contact with ILE 330 (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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131D GLY* 4.4 7.6 - - - -
134D GLN* 3.3 36.6 - - + +
309D GLU* 3.3 31.8 + - + +
311D ARG* 4.2 26.9 - - + +
328D PHE* 3.7 23.3 - - + -
329D ALA* 1.3 77.4 - - - +
331D THR* 1.3 65.6 + - - +
334D GLY 4.4 2.7 - - - -
335D ILE* 4.2 12.3 - - + +
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Residues in contact with THR 331 (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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134D GLN* 4.2 3.4 + - - -
169D ARG* 3.4 5.8 + - - -
176D ARG* 5.1 1.2 + - - -
309D GLU* 4.1 12.6 - - - +
329D ALA* 4.8 6.1 + - + -
330D ILE* 1.3 83.7 - - - +
332D ALA* 1.3 58.7 + - - +
333D GLY* 3.8 7.4 + - - -
334D GLY* 2.7 43.5 + - - -
336D GLY* 4.9 3.3 + - - -
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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