Contacts of the strand formed by residues 248 - 256 (chain A) in PDB entry 2ADU
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 CYS 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ILE* 4.9 6.1 - - - -
193A MET* 3.9 7.0 - - - -
196A ILE* 5.7 0.2 - - - -
223A CYS* 3.5 37.9 - - - -
224A SER 3.5 3.8 - - - -
225A LEU* 3.7 15.7 - - + -
242A LEU* 4.2 14.4 - - + -
246A ASP 3.8 0.8 - - - -
247A ILE* 1.3 72.6 - - - +
249A LYS* 1.3 61.9 + - - +
250A ILE* 3.6 16.0 + - - -
266A THR* 3.4 0.9 - - - -
267A VAL* 2.6 52.5 + - + +
269A PHE* 6.3 0.2 - - + -
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Residues in contact with LYS 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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222A GLY 2.9 15.9 - - - +
223A CYS* 3.0 10.9 - - - -
224A SER* 3.0 20.5 + - - +
226A ASN 3.2 8.1 + - - +
228A CYS 3.1 28.2 + - - -
229A ALA* 3.9 14.4 - - - +
247A ILE* 2.8 22.8 + - - +
248A CYS* 1.3 75.0 - - - +
250A ILE* 1.3 61.0 + - - +
251A ASP* 3.5 2.2 + - + +
265A PHE 3.7 4.5 - - - +
266A THR* 3.8 7.6 - - + +
366A PHE* 5.3 0.2 - - + -
455A THR* 3.1 36.9 + - - +
456A ALA* 4.0 7.2 - - - -
457A GLN* 3.7 42.4 - - + +
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Residues in contact with ILE 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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183A VAL* 5.0 2.2 - - + -
187A ILE* 4.4 13.0 - - + -
196A ILE* 4.5 13.2 - - + -
200A LEU* 3.9 17.7 - - + -
221A THR* 4.7 2.5 - - + -
222A GLY 3.2 3.8 - - - +
223A CYS* 4.1 13.0 - - + -
248A CYS* 3.6 20.6 + - - -
249A LYS* 1.3 69.8 - - - +
251A ASP* 1.3 60.2 + - - +
252A PHE* 3.7 20.3 + - + -
263A CYS 4.4 0.2 - - - +
264A ALA* 3.1 4.3 - - - +
265A PHE* 2.9 68.5 + - + +
267A VAL* 4.1 16.8 - - + -
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Residues in contact with ASP 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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219A PHE* 3.4 8.5 - - - -
222A GLY* 2.7 44.2 + - - +
230A ALA* 5.5 5.6 - - + +
249A LYS 3.5 2.4 + - - +
250A ILE* 1.3 73.1 - - - +
252A PHE* 1.3 62.8 + - - +
262A ASP* 3.0 6.4 - - - +
263A CYS 3.8 1.0 - - - +
264A ALA* 3.4 17.5 - - + +
364A GLU* 4.2 0.3 - - - +
457A GLN* 3.2 21.0 + - - +
459A GLU* 3.1 2.1 - - - +
501A CO 2.1 32.1 + - - -
906A R20 3.0 15.8 + - - -
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Residues in contact with PHE 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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176A HIS* 2.8 74.0 + + - -
179A VAL* 3.6 31.9 - - + -
180A ARG* 4.0 13.7 - - + -
200A LEU* 4.0 19.7 - - + -
204A SER* 4.7 6.5 - - - -
219A PHE* 3.4 12.6 - - - +
220A PRO 4.5 0.9 - - - +
221A THR* 4.2 21.5 - - + +
250A ILE* 3.7 27.6 - - + -
251A ASP* 1.3 76.2 + - - +
253A GLY* 1.3 66.8 + - - +
254A THR* 4.7 5.4 - - + -
263A CYS 3.1 11.2 + - - +
265A PHE* 4.3 2.5 - + - -
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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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176A HIS* 4.4 0.9 - - - -
217A LEU* 3.6 11.3 - - - +
218A ALA* 3.0 21.7 + - - -
219A PHE* 3.4 26.1 + - - +
252A PHE* 1.3 80.3 - - - +
254A THR* 1.3 66.6 + - - +
261A ILE 3.1 14.1 - - - -
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Residues in contact with THR 254 (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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172A ALA* 2.7 26.0 + - - +
175A ALA* 4.3 11.9 - - + -
176A HIS* 4.1 8.9 - - - +
179A VAL* 5.5 0.4 - - + -
204A SER* 3.5 24.7 - - - +
208A ILE* 3.7 22.2 - - + -
216A GLY 3.5 8.7 - - - +
218A ALA* 4.1 2.4 - - - +
252A PHE* 4.7 10.3 - - + -
253A GLY* 1.3 77.2 - - - +
255A HIS* 1.3 62.3 + - - +
260A ILE* 3.7 0.7 - - - -
261A ILE* 2.9 33.0 + - - +
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Residues in contact with HIS 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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172A ALA* 4.1 1.6 - - - -
208A ILE* 3.7 2.0 - - - +
212A GLY 4.8 1.2 + - - -
213A LEU* 3.3 35.1 - - - -
214A ASN 4.2 0.2 - - - -
215A ALA* 3.4 5.9 - - - -
216A GLY* 3.1 58.6 + - - +
217A LEU 3.9 8.4 + - - -
218A ALA* 3.9 2.9 - - + -
254A THR* 1.3 77.1 - - - +
256A ILE* 1.3 67.4 + - - +
257A SER 3.8 0.2 + - - -
258A GLY* 3.1 21.5 + - - -
259A ARG 3.5 20.4 - - - +
260A ILE* 4.0 11.9 - - + -
336A TYR* 3.9 7.0 - + - -
413A LEU* 3.5 25.3 - - + +
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Residues in contact with ILE 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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168A ASP* 3.4 37.9 - - + +
171A GLU* 3.5 43.3 - - + +
172A ALA* 4.1 2.9 - - - +
208A ILE* 3.7 21.1 - - + +
214A ASN 3.6 5.6 - - - +
215A ALA* 3.7 19.5 - - + -
255A HIS* 1.3 82.4 - - - +
257A SER* 1.3 80.0 + - - +
258A GLY 3.1 0.2 - - - -
259A ARG* 2.9 23.2 + - - +
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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