Contacts of the strand formed by residues 256 - 260 (chain A) in PDB entry 3ASW
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A GLY 3.8 12.9 + - - -
213A THR 3.1 8.6 + - - -
214A ASN* 3.5 47.4 + - + +
215A VAL* 2.8 29.6 + - - +
254A GLY 3.8 12.1 - - - -
255A ASP* 1.3 77.3 - - - +
257A PHE* 1.3 62.3 + - - +
258A THR* 4.3 11.4 - - + -
306A THR* 4.0 22.7 - - + -
307A PHE 3.1 17.3 - - - +
308A VAL* 3.9 11.2 - - + -
309A PHE* 4.5 1.6 - - - -
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Residues in contact with PHE 257 (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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215A VAL 4.5 0.4 - - - +
216A ASN* 3.3 20.0 - - - +
219A VAL* 3.8 33.0 - - + -
245A PHE* 4.0 36.3 - + + -
256A TYR* 1.3 74.3 - - - +
258A THR* 1.3 73.2 + - - +
294A ALA* 5.1 1.3 - - + -
306A THR* 3.6 0.9 - - - +
307A PHE* 2.8 76.9 + + + -
309A PHE* 3.7 35.2 - + - -
323A PHE* 4.6 4.0 - + - -
346A ILE* 4.6 12.1 - - + -
347A ALA* 4.3 6.3 - - + -
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Residues in contact with THR 258 (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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214A ASN* 4.6 2.7 - - - +
216A ASN* 3.1 25.3 + - - +
256A TYR* 4.3 17.9 - - + -
257A PHE* 1.3 85.3 - - - +
259A ALA* 1.3 63.6 + - - +
260A LYS* 6.0 0.3 - - - +
304A THR* 3.8 15.2 - - + +
305A TYR 3.0 13.7 - - - +
306A THR* 4.0 12.8 - - - +
307A PHE* 4.3 4.7 - - - -
345A ASN* 4.1 2.8 + - - +
346A ILE* 3.8 0.5 - - - +
347A ALA 3.0 25.3 + - - -
348A ASP 5.6 0.7 + - - -
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Residues in contact with ALA 259 (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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241A MET* 4.8 8.3 - - + -
258A THR* 1.3 76.9 - - - +
260A LYS* 1.3 58.1 + - - +
304A THR* 3.1 7.7 - - - -
305A TYR* 2.7 55.8 + - + -
307A PHE* 4.0 15.0 - - + -
323A PHE* 5.4 0.4 - - + -
344A ILE* 5.3 1.6 - - + -
345A ASN* 3.0 12.1 - - - +
346A ILE* 4.3 15.9 - - + -
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Residues in contact with LYS 260 (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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258A THR* 5.3 0.6 + - - +
259A ALA* 1.3 72.6 - - - +
261A LEU* 1.3 92.0 + - - +
262A PRO* 5.6 0.8 - - - +
263A ASP* 5.5 4.4 + - - -
302A THR* 3.0 29.6 + - - +
303A LYS* 3.6 9.1 - - - +
304A THR* 3.6 13.2 - - + +
343A ASN 4.4 0.9 - - - +
344A ILE* 3.8 4.6 - - - -
345A ASN* 2.8 48.8 + - + +
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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