Contacts of the strand formed by residues 325 - 328 (chain A) in PDB entry 2Y48
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 TYR 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A PHE* 4.3 10.8 - - + -
321A ARG* 3.5 2.4 - - - -
322A LYS* 2.9 37.2 + - + +
323A GLY* 4.6 1.4 - - - +
324A ASN* 1.3 80.6 - - - +
326A VAL* 1.3 65.5 + - - +
665A CYS* 3.5 45.8 - - + -
666A PHE 3.2 32.3 + - - -
667A ASP* 4.7 1.7 - - - -
700A ALA* 3.9 14.8 - - + -
701A PRO* 4.4 4.7 - - + -
702A ILE* 3.8 12.1 - - + -
744A LYS* 3.9 17.0 - - + +
745A GLU* 4.4 19.7 - - + -
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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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319A THR* 4.3 5.2 - - + -
320A PHE 3.2 4.7 - - - -
321A ARG* 3.8 25.1 - - + +
323A GLY 5.6 1.3 - - - +
324A ASN* 3.5 13.3 + - - +
325A TYR* 1.3 80.3 - - - +
327A ALA* 1.3 63.4 + - - +
568A ARG 4.0 8.3 - - - +
569A ASN* 3.5 32.1 - - - +
570A GLY* 3.7 11.2 - - - +
698A TYR* 3.2 27.0 - - + -
702A ILE* 3.4 8.5 - - - +
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Residues in contact with ALA 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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319A THR* 4.3 2.0 - - - -
320A PHE* 2.6 47.4 + - + +
326A VAL* 1.3 76.3 - - - +
328A ASP* 1.3 59.1 + - - +
329A LEU* 4.5 0.7 - - - +
663A VAL* 3.8 35.2 - - + -
698A TYR* 3.7 20.6 - - + -
702A ILE* 4.2 6.5 - - + -
704A LEU* 4.4 3.6 - - + -
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Residues in contact with ASP 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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318A ALA 3.4 7.3 - - - +
319A THR* 2.6 27.1 + - - +
327A ALA* 1.3 73.6 - - - +
329A LEU* 1.3 61.8 + - - +
330A GLY 3.3 2.2 - - - +
331A ALA 3.3 25.6 - - - +
332A MET* 4.4 11.0 - - + +
567A VAL* 4.2 5.5 + - - +
570A GLY* 4.0 5.5 - - - -
571A TYR* 2.8 28.4 + - - +
661A LYS* 3.5 17.5 + - - +
663A VAL* 5.0 0.7 - - - +
698A TYR* 3.0 27.7 + - - +
704A LEU* 4.0 10.4 - - - +
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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