Contacts of the strand formed by residues 249 - 257 (chain B) in PDB entry 4N41
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 ASP 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B ALA* 4.4 0.2 - - - +
246B ASP* 2.8 28.8 + - + +
247B PRO 3.0 1.0 - - - -
248B LYS* 1.3 79.8 - - + +
250B PRO* 1.3 59.3 - - - +
251B ARG* 3.1 46.9 + - - +
252B LYS* 3.6 15.8 + - + +
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Residues in contact with PRO 250 (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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203B GLU* 6.3 2.7 - - + -
245B ALA* 4.3 18.0 - - + +
246B ASP 3.1 8.9 - - - +
247B PRO* 3.9 9.5 - - + +
248B LYS 4.1 0.2 - - - -
249B ASP* 1.3 73.5 - - - +
251B ARG* 1.3 62.5 + - - +
252B LYS 3.4 1.5 - - - -
253B PRO* 5.2 1.2 - - - +
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Residues in contact with ARG 251 (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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248B LYS 4.7 3.2 + - - -
249B ASP* 3.3 31.4 - - - +
250B PRO* 1.3 82.8 - - - +
252B LYS* 1.3 87.2 + - - +
253B PRO* 3.4 9.9 - - - +
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Residues in contact with LYS 252 (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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245B ALA* 4.4 4.0 - - - +
246B ASP 4.8 0.2 + - - -
249B ASP* 3.6 12.9 + - + +
250B PRO 3.4 2.4 - - - -
251B ARG* 1.3 105.8 - - - +
253B PRO* 1.3 69.7 - - + +
254B ILE* 3.8 9.9 + - - +
20E G 6.1 2.2 - - - +
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Residues in contact with PRO 253 (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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205B LEU* 6.0 4.3 - - + -
243B TRP* 4.1 24.9 - - + -
244B VAL 3.7 7.9 - - - +
245B ALA* 5.0 3.1 - - + -
250B PRO 5.2 1.1 - - - +
251B ARG 3.4 10.3 - - - +
252B LYS* 1.3 89.4 - - + +
254B ILE* 1.3 59.6 + - - +
255B PRO* 4.5 1.9 - - - +
20E G 5.4 2.4 + - - -
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Residues in contact with ILE 254 (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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202B TRP* 3.9 26.2 - - + -
243B TRP* 3.7 4.0 - - - -
244B VAL* 2.8 54.5 + - + +
245B ALA* 3.7 11.4 - - - -
246B ASP* 4.1 6.7 - - + +
252B LYS 4.0 4.9 - - - +
253B PRO* 1.3 76.5 - - - +
255B PRO* 1.3 71.3 - - + +
20E G 4.1 22.2 - - - +
21E T 3.1 44.9 - - - +
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Residues in contact with PRO 255 (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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215B LEU* 5.8 6.3 - - + -
217B LEU* 4.7 14.8 - - + -
223B LEU* 5.8 5.6 - - + -
241B VAL* 4.7 8.7 - - + -
242B ALA 3.9 2.0 - - - +
243B TRP* 3.3 36.1 - - + -
253B PRO 4.5 1.1 - - - +
254B ILE* 1.3 85.4 - - - +
256B HIS* 1.3 63.0 + - - +
21E T 3.0 49.4 - - + +
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Residues in contact with HIS 256 (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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195B ASN* 3.1 14.5 + - - -
197B TYR* 2.9 29.5 + + - -
202B TRP* 4.0 11.0 - + - -
227B HIS* 3.8 12.9 - + - -
241B VAL* 3.6 3.5 - - - +
242B ALA* 2.9 35.4 + - - +
244B VAL* 4.3 10.1 - - + -
255B PRO* 1.3 73.7 - - - +
257B LEU* 1.3 88.5 + - - +
260B LEU* 4.2 14.8 - - + -
261B LEU* 3.4 37.6 - - + +
21E T 3.8 28.2 + - - -
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Residues in contact with LEU 257 (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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212B PRO* 4.4 21.3 - - + -
223B LEU* 5.0 9.9 - - + +
224B LEU* 4.3 22.0 - - + +
227B HIS* 4.3 17.0 - - + +
233B LEU* 5.2 4.9 - - + -
238B GLY* 4.8 12.8 - - - -
239B GLY 4.4 5.2 - - - +
240B ARG 3.8 12.1 - - - +
241B VAL* 4.6 8.5 - - + -
256B HIS* 1.3 93.0 + - - +
258B THR* 1.3 58.0 + - - +
259B GLY 3.0 7.0 - - - +
260B LEU* 2.8 46.7 + - + +
261B LEU* 3.0 16.0 + - - +
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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