Contacts of the strand formed by residues 270 - 275 (chain A) in PDB entry 2N5T
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 GLU 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A PRO* 5.7 0.4 - - - -
268A GLN* 5.7 4.5 - - - +
269A VAL* 1.3 75.8 - - - +
271A VAL* 1.3 66.0 + - - +
272A CYS* 4.6 10.5 - - - -
290A GLU* 3.3 10.3 - - + +
330A ILE* 6.1 0.3 - - - +
387A ARG* 5.8 2.1 + - - -
498A TRP* 5.4 8.5 - - - -
521A ASP 3.0 10.5 + - - +
522A GLU* 3.5 28.5 - - + +
523A PHE* 2.8 26.5 + - - -
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Residues in contact with VAL 271 (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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261A ALA* 3.4 28.7 - - + -
269A VAL* 4.1 6.5 - - + -
270A GLU* 1.3 82.2 - - - +
272A CYS* 1.3 62.7 + - - +
289A ALA* 3.8 2.8 - - - -
290A GLU* 2.6 42.5 + - - +
523A PHE* 3.3 8.5 - - + -
525A MET* 4.3 15.3 - - + -
530A ILE* 3.6 37.5 - - + +
533A ILE* 5.1 1.6 - - + -
534A LYS* 5.2 4.9 - - + +
537A ILE* 4.1 11.4 - - + -
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Residues in contact with CYS 272 (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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270A GLU* 4.6 14.6 - - - -
271A VAL* 1.3 81.7 - - - +
273A ALA* 1.3 60.8 + - - +
290A GLU 4.1 4.9 - - - +
291A GLY* 2.9 37.2 - - - +
292A VAL 3.9 2.9 - - - -
293A GLY* 3.5 20.0 - - - +
522A GLU* 5.0 5.2 - - + -
523A PHE 2.7 9.5 + - - +
524A SER* 3.2 6.5 - - - +
525A MET* 2.8 30.7 + - - +
530A ILE* 3.7 7.4 - - - +
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Residues in contact with ALA 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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272A CYS* 1.3 72.7 - - - +
274A ASN* 1.3 68.1 + - - +
275A ILE* 4.4 5.4 - - + -
284A ALA* 3.5 33.0 - - + -
289A ALA* 4.0 1.3 - - + +
291A GLY 3.1 6.5 + - - +
292A VAL* 3.3 10.4 - - + +
293A GLY 2.9 21.5 + - - -
524A SER* 3.2 5.4 - - - -
525A MET 3.1 8.7 - - - +
527A ALA* 4.2 7.0 - - + -
530A ILE* 3.9 11.8 - - + +
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Residues in contact with ASN 274 (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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273A ALA* 1.3 76.3 - - - +
275A ILE* 1.3 63.6 + - - +
280A ASP* 5.1 1.0 - - - +
294A LEU* 3.2 18.5 - - - +
296A ARG* 3.4 29.8 - - - +
502A CYS* 2.8 31.3 + - - +
504A GLU* 4.8 5.1 + - - -
524A SER* 2.6 39.2 + - - -
525A MET* 2.6 24.9 + - - +
526A SER* 4.2 6.5 - - - +
527A ALA 4.8 1.4 + - - -
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Residues in contact with ILE 275 (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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273A ALA* 4.4 9.2 - - + -
274A ASN* 1.3 78.5 - - - +
276A GLY* 1.3 60.8 + - - +
277A THR 4.3 5.4 - - - +
280A ASP* 3.3 37.9 - - + +
281A VAL* 4.3 12.8 - - + +
284A ALA* 4.8 0.2 - - + -
292A VAL* 3.6 42.8 - - + -
294A LEU 2.7 13.3 + - - +
295A TYR* 3.6 15.2 - - + -
296A ARG* 3.0 32.2 + - - +
320A VAL* 3.7 28.5 - - + -
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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