Contacts of the strand formed by residues 271 - 275 (chain A) in PDB entry 2AQ5
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 LEU 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A HIS* 4.3 0.7 - - - +
237A THR* 2.8 45.8 + - + -
238A GLY 5.8 0.4 - - - +
239A PHE* 5.3 1.8 - - - -
245A ARG* 3.4 49.8 - - + +
246A GLN 4.8 2.9 - - - +
264A LEU* 3.5 32.3 - - + -
269A GLY 3.5 0.8 + - - -
270A VAL* 1.3 75.7 - - - +
272A LEU* 1.3 62.1 + - - +
273A PRO* 3.6 2.4 - - - +
284A LEU* 4.4 24.2 - - + +
285A CYS* 3.8 5.4 - - - +
286A GLY 4.0 7.9 - - - +
289A ASP* 3.7 9.9 - - - +
293A ARG* 4.7 7.0 - - - +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP* 3.7 20.0 - - + +
37A SER 4.3 17.5 - - - +
38A GLY* 4.3 8.7 - - - +
225A HIS* 3.6 34.1 - - + +
270A VAL* 4.2 12.6 - - + +
271A LEU* 1.3 74.4 - - - +
273A PRO* 1.3 67.2 - - + +
274A PHE* 3.6 22.8 - - + -
284A LEU* 3.5 4.1 - - - -
285A CYS 2.7 38.2 + - - +
286A GLY* 5.2 1.1 - - - -
287A LYS* 5.7 6.5 - - + +
319A MET* 6.1 2.9 - - + -
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Residues in contact with PRO 273 (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 HIS* 4.0 22.4 - - + +
227A VAL* 3.8 40.9 - - + +
235A LEU* 3.9 16.2 - - + -
237A THR* 4.2 9.2 - - + -
271A LEU 3.6 8.1 - - - +
272A LEU* 1.3 86.4 - - + +
274A PHE* 1.3 65.7 + - - +
275A PHE 4.1 0.4 - - - -
282A VAL* 4.1 3.1 - - + -
283A TYR 3.3 5.6 - - - +
284A LEU* 3.8 17.3 - - + -
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY* 5.9 1.1 - - - -
272A LEU* 3.6 35.7 - - + -
273A PRO* 1.3 76.7 - - - +
275A PHE* 1.3 61.6 + - - +
282A VAL* 3.4 3.3 - - - -
283A TYR* 2.9 47.1 + - + +
285A CYS* 3.7 20.6 - - + -
319A MET* 4.1 27.6 - - + -
320A GLY* 5.4 0.2 - - - -
321A TYR* 3.8 50.0 - + + -
337A PHE* 4.0 11.0 - + - -
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A VAL* 4.6 10.7 - - + +
228A PHE 3.6 21.5 - - - +
229A VAL* 3.5 40.4 - - + -
230A SER* 3.5 12.3 - - - -
273A PRO 4.1 1.4 - - - -
274A PHE* 1.3 74.9 - - - +
276A ASP* 1.3 62.6 + - - +
277A PRO* 3.5 38.6 - - + +
280A ASN* 3.4 45.1 - - - -
281A ILE 3.6 9.4 - - - -
282A VAL* 4.4 5.2 - - + +
297A ILE* 4.1 8.3 - - + -
321A TYR* 4.5 8.0 + - - -
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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