Contacts of the strand formed by residues 248 - 253 (chain A) in PDB entry 1Y24
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 PHE 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLY 3.2 5.8 - - - -
221A PRO* 3.3 23.3 - - + -
223A ASP* 5.6 5.8 - - + -
231A SER* 3.2 32.5 - - - -
234A SER* 5.4 0.4 - - - -
235A TRP* 3.5 35.4 - + + -
247A PHE* 1.3 74.1 - - - +
249A THR* 1.3 96.7 + - - +
250A GLY* 4.0 5.4 - - - -
282A GLN* 3.5 38.4 - - + -
285A GLN* 5.7 0.2 - - - -
294A PRO 2.8 8.3 + - - +
295A ILE* 3.7 25.6 - - + -
296A TYR* 2.7 32.6 + - - +
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Residues in contact with THR 249 (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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130A PHE* 3.7 7.9 - - + -
178A GLU* 2.7 27.5 + - - +
220A GLY* 2.9 17.9 + - - -
222A GLY* 2.8 32.7 + - - -
223A ASP 3.4 4.0 + - - -
247A PHE* 3.5 25.1 - - + -
248A PHE* 1.3 98.1 - - - +
250A GLY* 1.3 57.8 + - - +
296A TYR* 3.2 4.9 - - + -
298A ASP* 3.0 24.9 - - - +
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Residues in contact with GLY 250 (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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222A GLY* 5.0 1.3 - - - -
223A ASP 3.2 11.2 - - - -
248A PHE* 4.0 8.4 - - - -
249A THR* 1.3 76.3 - - - +
251A GLU* 1.3 59.9 + - - -
282A GLN* 5.9 1.3 - - - -
296A TYR 3.0 7.5 + - - -
297A ASN* 3.1 40.0 + - - +
298A ASP* 3.5 6.6 + - - +
299A GLU* 5.1 0.7 - - - -
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Residues in contact with GLU 251 (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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182A GLU* 3.0 27.6 - - + +
185A HIS* 5.2 0.9 - - - -
222A GLY 5.1 2.0 - - - +
223A ASP 2.8 8.6 + - - +
224A SER* 3.1 30.9 - - - +
225A PHE* 3.0 42.3 + - - +
250A GLY* 1.3 71.4 - - - -
252A ALA* 1.3 74.5 + - - +
253A GLY 3.2 15.2 + - - -
278A VAL* 5.6 1.2 - - - +
297A ASN* 5.2 0.2 - - - -
299A GLU* 3.3 34.7 - - + +
301A ASP* 4.7 0.5 - - - +
304A VAL* 3.6 23.5 - - - +
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Residues in contact with ALA 252 (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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225A PHE* 4.3 1.8 - - - -
250A GLY 4.1 0.2 + - - -
251A GLU* 1.3 76.1 + - - +
253A GLY* 1.3 57.8 + - - +
275A GLN* 3.1 36.5 + - + +
278A VAL* 4.0 18.2 - - + -
279A VAL* 6.3 0.9 - - + -
297A ASN* 4.9 15.9 - - - +
299A GLU 2.7 12.1 + - - +
300A ALA* 3.3 9.1 - - + -
301A ASP* 3.1 18.0 + - - +
334A LEU* 5.5 1.3 - - + -
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Residues in contact with GLY 253 (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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225A PHE* 3.6 24.7 - - - +
251A GLU* 3.2 5.1 + - - -
252A ALA* 1.3 73.6 - - - +
254A VAL* 1.3 60.9 - - - -
255A ARG 3.4 7.7 + - - +
270A ILE* 5.5 0.2 - - - +
275A GLN* 4.5 1.1 - - - -
278A VAL* 5.7 2.2 - - - +
301A ASP* 3.6 9.9 - - - -
302A PRO 3.7 5.8 - - - -
304A VAL* 3.7 19.1 - - - -
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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