Contacts of the strand formed by residues 237 - 249 (chain A) in PDB entry 2AEX
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 PRO 237 (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 3.2 10.1 - - - +
213A ASN* 3.6 13.9 - - - +
232A LYS* 3.6 28.9 - - + +
235A LYS* 3.6 10.5 - - + +
236A LEU* 1.3 87.7 - - - +
238A PHE* 1.3 56.6 + - - +
266A VAL* 3.3 2.4 - - - -
267A GLU* 2.7 59.2 + - + +
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Residues in contact with PHE 238 (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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210A VAL* 4.1 25.1 - - + -
211A HIS* 3.5 5.2 - - - +
212A GLY* 2.7 57.8 + - - +
213A ASN 3.7 11.7 - - - -
214A LEU* 3.6 27.4 - - + -
215A SER 5.5 0.2 - - - -
236A LEU 4.1 2.5 - - - +
237A PRO* 1.3 75.4 - - - +
239A CYS* 1.3 66.2 + - - +
240A ALA* 4.1 19.1 - - + -
264A PHE* 3.6 29.6 - + + -
265A GLU* 3.1 14.8 - - - +
266A VAL* 4.1 4.0 - - + -
267A GLU* 6.0 0.2 - - - -
408A PHE* 4.5 9.0 - + - -
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Residues in contact with CYS 239 (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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149A LYS* 3.6 29.4 - - + -
209A VAL* 4.5 0.9 - - - -
210A VAL 3.3 10.3 - - - +
211A HIS* 3.6 24.7 - - + -
238A PHE* 1.3 77.2 - - - +
240A ALA* 1.3 64.0 + - - +
241A MET* 3.5 31.6 - - - -
263A TYR* 4.1 2.1 - - - +
264A PHE* 3.4 3.8 - - - -
265A GLU* 2.9 38.0 + - + +
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Residues in contact with ALA 240 (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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209A VAL* 3.6 0.3 - - - -
210A VAL* 2.9 33.3 + - + +
238A PHE* 3.9 9.1 - - + -
239A CYS* 1.3 75.8 - - - +
241A MET* 1.3 63.1 + - - +
263A TYR 3.4 7.2 - - - +
264A PHE* 3.9 17.7 - - + -
407A LEU* 3.7 25.5 - - + +
408A PHE* 4.0 14.4 - - + -
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Residues in contact with MET 241 (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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149A LYS* 3.6 26.2 - - + +
152A MET* 3.6 25.1 - - + +
153A GLU* 3.5 36.6 - - + +
156A ILE* 4.0 3.6 - - + -
208A SER 3.1 13.5 - - - +
209A VAL* 3.9 17.5 - - + -
211A HIS* 5.7 0.2 - - + -
239A CYS* 3.5 28.3 - - - -
240A ALA* 1.3 76.5 - - - +
242A GLY* 1.3 59.0 + - - +
262A ARG* 3.2 5.2 - - - +
263A TYR* 2.9 41.6 + - + +
407A LEU* 3.9 7.9 - - - +
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Residues in contact with GLY 242 (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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156A ILE* 3.9 11.4 - - - +
207A ILE* 3.2 6.1 - - - +
208A SER* 3.0 32.1 + - - +
241A MET* 1.3 77.2 - - - +
243A VAL* 1.3 60.9 + - - -
261A TYR 3.1 13.0 - - - -
262A ARG* 3.9 6.5 - - - -
407A LEU* 3.9 9.7 - - - +
500A CIT 6.1 0.2 - - - -
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Residues in contact with VAL 243 (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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156A ILE* 3.9 23.0 - - + +
159A THR* 4.5 8.7 - - + -
160A GLN* 4.6 4.5 - - + +
205A VAL* 4.2 15.5 - - + -
206A SER 3.2 13.7 - - - +
207A ILE* 3.8 15.0 - - + -
242A GLY* 1.3 75.2 - - - -
244A SER* 1.3 65.8 + - - +
259A PHE* 4.1 25.4 - - + -
260A ASN* 3.1 4.7 - - - +
261A TYR* 2.9 54.1 + - + +
358A ALA* 6.0 0.2 - - + -
500A CIT 4.7 1.6 - - - +
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Residues in contact with SER 244 (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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206A SER* 2.9 44.9 + - - -
243A VAL* 1.3 79.2 - - - +
245A SER* 1.3 61.7 + - - +
259A PHE 3.3 7.2 - - - -
413A ARG* 5.7 0.2 + - - -
416A SER* 4.9 4.3 - - - -
419A MET* 3.4 11.6 - - - +
500A CIT 3.6 45.0 + - - -
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Residues in contact with SER 245 (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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204A GLY 2.7 20.3 + - - -
205A VAL* 3.6 9.6 - - - +
244A SER* 1.3 75.9 - - - +
246A VAL* 1.3 66.2 + - - +
247A ILE* 3.6 17.2 - - - +
257A ILE 4.6 0.2 - - - -
258A HIS* 3.3 7.0 - - - -
259A PHE* 2.9 66.4 + - - -
419A MET* 3.7 2.8 - - - +
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Residues in contact with VAL 246 (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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202A LYS* 4.3 1.2 - - - +
203A ALA* 3.6 1.9 - - - -
204A GLY* 3.0 26.7 + - - -
245A SER* 1.3 79.4 + - - +
247A ILE* 1.3 64.4 + - - +
248A HIS* 3.4 34.4 - - + +
256A THR* 4.4 0.2 - - + -
257A ILE 3.4 9.0 - - - +
258A HIS* 3.8 11.9 - - + -
392A TYR* 3.4 27.8 - - + +
416A SER 5.5 0.2 - - - +
419A MET* 3.6 13.0 - - + +
420A SER* 3.6 31.9 - - - +
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Residues in contact with ILE 247 (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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163A VAL* 4.1 10.8 - - + -
167A LEU* 3.8 32.8 - - + -
200A PHE* 3.4 38.4 - - + -
202A LYS 3.7 2.7 - - - -
203A ALA* 4.2 9.4 - - + -
204A GLY 4.6 1.1 - - - +
245A SER* 3.6 18.6 - - - +
246A VAL* 1.3 79.6 - - - +
248A HIS* 1.3 60.9 + - - +
249A PRO* 3.6 1.0 - - - +
256A THR* 3.2 8.8 - - - +
257A ILE* 2.9 49.6 + - + -
259A PHE* 4.7 4.0 - - + -
361A VAL* 6.0 1.1 - - + -
365A TYR* 3.6 14.3 + - + +
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Residues in contact with HIS 248 (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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200A PHE* 3.6 3.3 - - - -
201A GLU* 2.9 35.3 + - + +
202A LYS* 2.8 22.0 + - + +
246A VAL* 3.4 15.7 - - + +
247A ILE* 1.3 70.7 - - - +
249A PRO* 1.3 64.9 - - - +
256A THR* 2.8 36.6 + - + +
389A ARG* 3.4 20.1 + - - -
392A TYR* 4.1 17.5 - + + -
419A MET 5.7 0.7 - - - -
420A SER 2.8 27.4 + - - -
421A LEU 4.0 3.6 - - - -
422A PRO* 3.5 30.4 - - + -
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Residues in contact with PRO 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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199A VAL* 3.4 11.7 - - + +
200A PHE* 4.1 13.7 - - + -
201A GLU* 3.8 0.8 - - - +
247A ILE 3.6 1.6 - - - +
248A HIS* 1.3 84.2 - - - +
250A LYS* 1.3 64.5 + - - +
251A ASN 4.2 1.7 - - - +
254A ALA* 3.4 34.1 - - + +
255A PRO 3.2 30.1 - - - +
365A TYR* 3.2 15.3 - - - +
369A VAL* 4.5 3.6 - - + -
385A GLN* 3.3 1.7 - - - +
389A ARG* 2.8 41.6 + - - +
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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