Contacts of the strand formed by residues 248 - 256 (chain C) in PDB entry 2AYN
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 VAL 248 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246C PHE 3.8 6.3 - - - +
247C GLY* 1.3 72.3 - - - -
249C GLU* 1.3 70.7 + - - +
250C PHE* 3.2 34.5 - - + -
270C ASN* 3.1 7.3 - - - +
271C GLN* 2.8 36.3 + - + +
272C LEU 5.3 3.4 - - - +
273C GLN 5.7 0.4 - - - +
274C LEU* 5.2 5.6 - - + -
316C ILE* 3.9 16.2 - - + -
318C ARG 3.5 11.2 - - - +
320C PRO* 3.5 31.4 - - + -
323C LEU* 3.6 14.6 - - + -
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Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C GLY 5.3 1.1 - - - -
248C VAL* 1.3 78.2 - - - +
250C PHE* 1.3 67.6 + - - +
268C LYS* 6.2 0.6 - - + +
269C GLU 3.1 5.8 - - - +
270C ASN* 3.1 21.5 - - - +
316C ILE* 3.2 12.1 - - - +
317C SER* 2.8 42.0 + - - -
318C ARG* 3.2 35.7 + - + +
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Residues in contact with PHE 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C VAL* 3.2 29.8 - - + -
249C GLU* 1.3 76.8 - - - +
251C GLU* 1.3 65.4 + - - +
252C THR* 4.1 15.3 - - + -
268C LYS* 3.3 10.7 - - - +
269C GLU* 2.7 44.7 + - + +
271C GLN* 3.8 31.4 - - + -
274C LEU* 3.5 29.2 - - + -
293C LEU* 4.0 21.1 - - + -
314C SER* 4.6 6.5 - - - -
315C LYS 3.2 11.7 - - - +
316C ILE* 3.7 27.8 - - + -
317C SER* 3.8 3.3 - - - +
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Residues in contact with GLU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C PHE* 1.3 76.5 - - - +
252C THR* 1.3 61.9 - - - +
253C THR* 3.9 8.3 + - + +
267C GLY 3.2 6.5 - - - +
268C LYS* 4.1 26.1 + - + -
313C SER 3.7 3.3 - - - +
315C LYS* 2.9 25.9 + - - +
317C SER* 3.5 24.6 + - - -
359C THR* 3.6 31.0 + - + +
361C GLU* 4.6 13.7 - - - +
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Residues in contact with THR 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C PHE* 4.1 8.5 - - + -
251C GLU* 1.3 75.3 - - - +
253C THR* 1.3 63.2 + - - +
254C MET 4.2 0.6 + - - -
265C THR 3.6 1.7 - - - +
266C LYS* 3.3 2.6 - - - -
267C GLY* 2.6 48.9 + - - -
269C GLU* 4.1 26.2 + - + +
312C LYS* 3.9 25.7 - - - -
313C SER 3.5 4.9 - - - -
314C SER* 3.6 26.7 - - - +
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Residues in contact with THR 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C GLU* 4.7 7.9 - - + +
252C THR* 1.3 79.0 - - - +
254C MET* 1.3 59.9 + - - +
255C LYS* 3.8 2.1 + - - +
264C VAL* 4.4 12.7 - - - +
265C THR 3.4 5.6 - - - -
266C LYS* 3.5 37.9 - - + +
267C GLY 5.2 0.2 - - - +
311C ILE 3.5 2.3 - - - +
312C LYS* 4.5 1.8 - - - -
313C SER* 2.9 42.9 + - - -
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Residues in contact with MET 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C THR 4.2 0.6 + - - -
253C THR* 1.3 71.9 - - - +
255C LYS* 1.3 58.7 + - - +
256C CYS 3.9 1.0 + - - -
263C GLU 4.9 1.4 - - - +
264C VAL* 3.5 12.3 - - - +
265C THR* 3.0 36.0 + - - +
297C ILE* 3.8 36.6 - - - -
299C LYS* 3.0 39.3 - - + +
310C TYR* 3.8 28.0 - - + -
311C ILE 3.3 11.9 - - - +
312C LYS* 4.2 12.3 - - + +
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Residues in contact with LYS 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C THR* 3.8 1.9 + - - +
254C MET* 1.3 72.9 - - - +
256C CYS* 1.3 68.0 + - - +
257C THR 3.4 0.5 + - - -
264C VAL* 3.7 34.4 - - + +
310C TYR* 3.3 1.9 - - - -
311C ILE* 2.7 46.0 + - + +
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Residues in contact with CYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C MET 3.9 0.4 + - - -
255C LYS* 1.3 77.4 - - - +
257C THR* 1.3 70.8 + - - +
258C GLU* 3.6 27.5 - - - +
259C SER* 4.4 2.4 + - - +
260C GLU* 4.1 16.1 - - - +
262C GLU* 3.8 19.1 - - + +
264C VAL* 5.9 0.4 - - - +
301C SER* 5.0 0.9 - - - -
304C LEU* 5.5 0.7 - - - -
308C ALA* 4.5 7.4 - - - -
309C LEU 4.0 6.1 - - - -
310C TYR* 3.2 40.8 - - + -
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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