Contacts of the strand formed by residues 270 - 275 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269B VAL* 1.3 76.1 - - - +
271B VAL* 1.3 66.7 + - - +
272B CYS* 4.6 11.6 - - - -
290B GLU* 3.6 14.8 - - + +
330B ILE* 6.1 0.2 - - - +
387B ARG* 5.8 2.1 + - - -
498B TRP* 5.4 8.7 - - - -
521B ASP 3.0 10.0 + - - +
522B GLU* 3.5 28.5 - - + +
523B PHE* 2.8 26.7 + - - -
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B PRO* 6.4 1.1 - - + -
261B ALA* 3.7 25.1 - - + -
269B VAL* 4.0 8.3 - - + -
270B GLU* 1.3 83.7 - - - +
272B CYS* 1.3 62.6 + - - +
288B GLY 4.7 0.7 - - - +
289B ALA* 3.8 3.4 - - - -
290B GLU* 3.0 33.1 + - - +
523B PHE* 3.3 7.2 - - + -
525B MET* 4.3 15.9 - - + -
530B ILE* 3.7 37.2 - - + +
533B ILE* 5.2 0.4 - - + -
534B LYS* 5.2 7.9 - - + +
537B ILE* 4.1 13.9 - - + -
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Residues in contact with CYS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B GLU* 4.6 14.8 - - - -
271B VAL* 1.3 82.2 - - - +
273B ALA* 1.3 62.5 + - - +
290B GLU* 4.1 3.8 - - - +
291B GLY* 2.9 37.9 - - - +
292B VAL 3.9 2.5 - - - -
293B GLY* 3.5 21.1 - - - +
328B ALA 5.7 0.2 - - - -
522B GLU* 5.0 5.4 - - + -
523B PHE 2.7 9.7 + - - +
524B SER* 3.2 5.5 - - - +
525B MET* 2.8 30.7 + - - +
530B ILE* 3.7 6.5 - - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B CYS* 1.3 73.4 - - - +
274B ASN* 1.3 67.5 + - - +
275B ILE* 4.4 4.9 - - + -
284B ALA* 3.5 33.0 - - + -
289B ALA* 4.0 0.8 - - + +
291B GLY 3.1 6.5 + - - +
292B VAL* 3.3 10.1 - - + +
293B GLY 2.9 22.0 + - - -
524B SER* 3.2 5.2 - - - -
525B MET 3.1 8.1 - - - +
527B ALA* 4.2 6.5 - - + -
530B ILE* 3.9 11.1 - - + +
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Residues in contact with ASN 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ALA* 1.3 75.8 - - - +
275B ILE* 1.3 64.2 + - - +
280B ASP* 5.1 1.0 - - - +
294B LEU* 3.2 18.5 - - - +
296B ARG* 3.4 28.6 - - - +
502B CYS* 2.8 31.1 + - - +
504B GLU* 4.8 5.1 + - - -
524B SER* 2.6 39.8 + - - -
525B MET* 2.6 23.8 + - - +
526B SER* 4.2 7.0 - - - +
527B ALA* 4.8 1.6 + - - +
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ALA* 4.4 7.4 - - + -
274B ASN* 1.3 77.6 - - - +
276B GLY* 1.3 60.5 + - - +
277B THR 4.3 5.6 - - - +
280B ASP* 3.3 39.3 - - + +
281B VAL* 4.3 11.0 - - + +
284B ALA* 4.8 0.7 - - + -
292B VAL* 3.7 41.3 - - + -
294B LEU 2.7 13.5 + - - +
295B TYR* 3.6 15.4 - - + -
296B ARG* 3.0 33.2 + - - +
320B VAL* 3.7 30.3 - - + -
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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