Contacts of the strand formed by residues 324 - 328 (chain A) in PDB entry 1YQZ
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 ASN 324 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU* 3.3 41.1 - - + +
187A MET* 6.0 0.3 - - - +
294A LEU* 3.8 20.6 - - + -
322A GLY 3.0 14.1 + - - +
323A ASN* 1.3 79.0 + - - +
325A ILE* 1.3 69.6 + - - +
333A PHE 5.0 1.7 - - - +
334A ALA* 3.3 2.8 - - - +
335A SER* 2.9 69.5 + - - +
418B ALA* 4.5 2.5 - - - +
419B TYR 5.2 2.2 - - - +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A TYR* 4.6 9.8 - - - -
324A ASN* 1.3 81.5 + - - +
326A VAL* 1.3 66.8 + - - +
332A THR* 3.6 17.9 - - + -
333A PHE 3.2 13.9 - - - +
334A ALA* 3.7 11.0 - - + -
393A ASP* 3.5 32.3 - - + -
439A FAD 5.4 0.3 + - - -
418B ALA* 3.7 22.0 - - + +
419B TYR 3.6 31.2 + - - +
420B ALA* 3.6 16.9 - - + +
423B TYR* 3.8 20.2 - - + -
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A TYR* 3.7 26.7 - - + +
161A LEU* 5.3 6.3 - - + -
162A GLU* 3.5 28.9 - - + +
184A ASN* 3.8 31.6 - - - +
195A ILE* 6.0 0.2 - - + -
325A ILE* 1.3 76.2 - - - +
327A LYS* 1.3 72.6 + - - +
328A PHE* 5.4 2.2 - - + -
332A THR* 3.6 3.3 - - - +
333A PHE* 3.0 46.4 + - + +
420B ALA* 4.7 2.7 - - - -
423B TYR* 3.8 7.4 + - - -
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Residues in contact with LYS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A TYR* 4.9 14.2 + - - +
162A GLU* 4.3 11.4 + - - +
165A GLU* 2.9 38.0 + - - +
326A VAL* 1.3 87.8 - - - +
328A PHE* 1.3 64.8 + - - +
329A PHE 2.7 31.3 + - - +
331A TYR 3.5 4.9 - - - +
362B TYR* 3.7 25.1 - - - +
420B ALA* 5.3 1.2 - - - +
422B PRO* 3.9 16.4 - - + -
423B TYR* 3.1 29.1 + - + +
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.4 50.3 - - + -
164A LEU* 4.0 7.6 - - + -
165A GLU* 3.6 6.1 - - + -
195A ILE* 3.5 51.1 - - + -
198A GLU* 4.0 7.2 - - + +
199A LEU* 3.7 21.3 - - + -
326A VAL* 4.1 3.7 + - + -
327A LYS* 1.3 74.3 - - - +
329A PHE* 1.3 103.3 + + - +
330A ASP 3.2 1.0 + - - -
331A TYR* 2.9 26.1 + - - +
333A PHE* 3.8 16.6 - + + -
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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