Contacts of the strand formed by residues 252 - 257 (chain A) in PDB entry 1YZ3
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 ASP 252 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A THR* 5.0 0.7 + - - -
250A VAL* 3.3 7.9 - - - +
251A ARG* 1.3 82.9 - - - +
253A LEU* 1.3 67.4 + - - +
254A ARG* 3.2 32.6 + - - +
274A PHE* 3.8 12.6 - - - -
275A ALA* 3.4 3.1 - - - -
276A TRP* 2.7 52.5 + - + +
240B ARG* 3.9 24.1 + - - -
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLU* 3.2 45.2 - - + +
239A VAL* 4.6 13.2 - - + -
240A ARG* 5.2 11.0 - - + +
243A LEU* 4.7 6.3 - - + -
250A VAL* 4.2 13.2 - - + +
252A ASP* 1.3 80.3 + - - +
254A ARG* 1.3 76.1 + - - +
255A THR* 4.5 0.4 - - - +
273A PHE* 4.6 7.9 - - + -
274A PHE 3.1 6.5 - - - +
275A ALA* 3.2 33.7 - - + -
236B GLU* 3.9 6.1 - - - +
240B ARG* 4.1 3.3 + - - -
253B LEU 3.9 14.2 - - - +
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Residues in contact with ARG 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 3.8 16.8 - - + +
59A ARG* 5.3 1.4 - - - +
60A CYS* 4.1 34.7 + - - +
63A GLN* 2.8 41.9 + - - +
64A THR* 5.0 3.2 + - - +
236A GLU* 4.6 0.2 - - - -
252A ASP* 3.2 27.8 + - - +
253A LEU* 1.3 81.0 - - - +
255A THR* 1.3 62.4 + - - +
273A PHE* 3.2 7.3 - - - +
274A PHE* 2.8 39.0 + - + +
236B GLU* 3.5 13.5 - - - +
237B GLU* 4.4 22.8 + - - +
240B ARG* 4.1 19.9 - - - +
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Residues in contact with THR 255 (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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56A TRP* 3.8 9.0 + - - -
217A LEU* 3.6 29.2 - - + +
236A GLU* 2.6 31.4 + - - +
253A LEU* 4.5 0.2 - - - +
254A ARG* 1.3 75.4 + - - +
256A TYR* 1.3 71.5 + - - +
257A ILE* 4.2 10.4 + - + +
272A VAL 3.4 2.7 - - - -
273A PHE* 4.5 0.3 - - - +
236B GLU* 3.0 31.1 + - - +
255B THR* 3.8 22.7 - - + +
257B ILE* 4.5 4.9 - - + -
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Residues in contact with TYR 256 (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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51A ASN* 2.6 31.0 + - - -
52A GLY* 3.3 7.9 - - - -
53A VAL* 3.2 38.3 + - + -
56A TRP* 3.5 46.4 - + + +
59A ARG* 6.0 0.2 - - - -
255A THR* 1.3 77.0 - - - +
257A ILE* 1.3 65.2 + - - +
258A MET* 3.8 16.8 - - + -
259A PRO* 3.1 36.6 - - + +
262A LEU* 3.7 0.9 - - - +
271A GLY* 3.0 5.0 - - - -
272A VAL* 2.7 44.0 + - + +
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Residues in contact with ILE 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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255A THR* 4.2 15.4 + - + +
256A TYR* 1.3 85.6 - - - +
258A MET* 1.3 70.6 + - - +
259A PRO* 3.4 10.2 - - - +
270A LYS 4.1 9.2 - - - +
271A GLY* 4.3 0.7 - - - -
217B LEU* 4.0 36.6 - - + -
218B GLU* 4.3 22.0 + - + +
255B THR* 4.6 3.1 - - + -
257B ILE* 4.7 11.9 - - + -
270B LYS* 4.0 24.7 - - + +
271B GLY* 4.2 17.0 - - - +
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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