Contacts of the strand formed by residues 290 - 296 (chain B) in PDB entry 2NTZ
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 PHE 290 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A ALA* 5.5 1.8 - - + -
280B GLU* 4.3 9.4 - - - +
283B LYS* 5.6 0.2 - - - +
284B PHE* 4.0 12.1 - - - -
287B LYS 5.9 0.2 - - - -
288B ASP* 5.8 0.9 - - - -
289B ARG* 1.3 82.9 - - - +
291B ALA* 1.3 62.5 + - - +
292B ARG* 3.4 50.3 - - + +
303B GLU* 3.2 31.0 - - + -
304B PHE* 3.0 3.8 - - - +
305B ASN* 2.6 72.7 + - + +
307B LEU* 4.4 1.4 - - - +
31Y T 4.0 19.5 - - - -
32Y C 6.0 1.6 - - - -
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Residues in contact with ALA 291 (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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323A LEU* 4.7 8.3 - - + -
280B GLU* 3.0 18.4 + - - +
281B LEU* 2.9 24.4 + - + +
282B TRP* 4.1 11.0 + - + -
284B PHE* 4.1 18.8 - - + -
290B PHE* 1.3 75.8 - - - +
292B ARG* 1.3 61.5 + - - +
303B GLU 3.5 5.2 - - - -
304B PHE* 3.6 21.8 - - + -
307B LEU* 5.0 0.9 - - + -
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Residues in contact with ARG 292 (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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278B VAL* 5.2 14.0 - - + +
279B THR 4.2 3.8 - - - +
280B GLU* 3.0 32.6 + - - +
281B LEU* 2.8 16.1 - - - +
290B PHE* 3.4 39.1 - - + +
291B ALA* 1.3 78.0 - - - +
293B LYS* 1.3 63.2 + - - +
294B ARG* 4.6 7.9 - - - +
302B TYR* 3.4 4.5 - - - +
303B GLU* 2.8 54.1 + - + +
304B PHE* 4.8 1.1 - - - -
30Y A 4.3 2.2 + - - -
31Y T 2.7 41.0 + - - -
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Residues in contact with LYS 293 (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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309A LYS* 6.1 1.8 - - - +
312A GLN* 2.7 31.4 + - - +
316A ASP* 3.1 27.3 + - - +
278B VAL* 3.3 6.2 - - - +
279B THR* 3.0 44.4 + - + +
281B LEU* 3.8 12.4 - - + +
292B ARG* 1.3 77.0 - - - +
294B ARG* 1.3 68.4 + - - +
295B VAL* 3.3 25.6 - - + +
300B PHE* 4.6 2.0 - - - -
301B SER 3.5 7.6 - - - +
302B TYR* 3.8 22.9 - - + +
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Residues in contact with ARG 294 (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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275B LYS 5.2 6.1 - - - +
276B SER* 5.6 6.8 - - - +
277B VAL 3.5 8.1 - - - +
278B VAL* 4.1 21.3 - - + +
292B ARG* 4.6 7.0 - - + +
293B LYS* 1.3 78.1 - - - +
295B VAL* 1.3 72.8 + - - +
296B LYS* 5.3 5.8 - - + -
300B PHE* 3.2 3.8 - - - +
301B SER* 2.7 50.8 + - - +
303B GLU* 3.1 37.5 + - - +
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLN* 4.4 7.9 - - - +
275B LYS 3.5 13.0 - - - +
277B VAL* 3.1 32.3 + - + +
279B THR* 5.6 2.2 - - - +
293B LYS* 3.3 35.9 - - + +
294B ARG* 1.3 75.8 - - - +
296B LYS* 1.3 70.8 + - - +
297B GLY 4.2 11.0 - - - +
299B ALA 3.6 8.3 - - - +
300B PHE* 4.3 8.3 - - + -
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Residues in contact with LYS 296 (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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275B LYS* 4.0 46.0 - - - +
277B VAL* 5.8 0.4 - - - -
294B ARG* 5.3 7.9 - - + -
295B VAL* 1.3 78.1 - - - +
297B GLY* 1.3 74.4 + - - +
298B ARG 3.1 0.3 + - - -
299B ALA* 2.7 29.5 + - + +
32E C 5.0 12.0 + - - +
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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