Contacts of the strand formed by residues 285 - 294 (chain B) in PDB entry 4ND1
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 ILE 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ALA 3.3 1.2 - - - +
274B PHE* 3.7 10.5 - - - -
275B CYS* 2.7 33.9 + - - +
281B VAL* 3.8 36.6 - - + -
283B GLY* 1.3 74.6 - - - +
286B TYR* 1.3 68.6 + - - +
287B MET* 3.7 15.8 + - + -
319B ILE* 3.9 25.8 - - + +
322B VAL* 4.3 18.6 - - + -
323B ASN* 3.4 26.7 - - - +
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Residues in contact with TYR 286 (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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143B ASP* 3.9 30.5 - - - +
146B VAL* 3.3 23.1 - - + -
147B SER* 3.7 27.2 + - - -
150B GLN* 3.6 35.7 - - + +
157B HIS* 3.0 25.0 + + - -
160B VAL* 3.1 21.4 + - - +
272B SER* 3.6 7.2 - - - +
273B ALA* 3.4 18.8 - - - -
274B PHE* 3.4 37.4 - + + -
285B ILE* 1.3 79.6 - - - +
287B MET* 1.3 62.8 + - - +
322B VAL* 4.0 6.8 - - - +
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Residues in contact with MET 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 3.5 10.1 - - - +
193B GLY* 4.6 8.1 - - - -
194B GLY* 4.9 1.8 - - - +
272B SER* 3.7 7.9 + - - -
273B ALA 3.0 24.9 + - - +
275B CYS* 4.1 6.7 - - + -
279B TYR* 3.7 30.5 - - + -
281B VAL* 4.0 19.1 - - + -
285B ILE* 4.3 17.7 - - + -
286B TYR* 1.3 76.1 - - - +
288B GLY* 1.3 64.3 + - - +
289B VAL* 3.2 25.5 + - + +
315B LEU* 4.4 15.9 - - + -
319B ILE* 3.8 30.1 - - + -
322B VAL* 5.5 4.5 - - + -
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 3.6 4.4 + - - -
164B ALA* 6.2 2.0 - - - -
165B GLY* 5.9 4.9 - - - -
191B VAL 5.1 1.8 - - - -
192B ILE* 3.3 12.1 - - - +
193B GLY* 2.8 44.8 + - - -
270B PRO* 5.7 0.7 - - - -
271B CYS* 3.4 13.5 - - - -
272B SER* 4.1 1.6 - - - -
287B MET* 1.3 73.2 - - - +
289B VAL* 1.3 65.8 + - - +
315B LEU* 5.3 0.2 - - - +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 4.4 2.5 - - + -
270B PRO* 4.0 5.4 - - - -
271B CYS 2.9 29.2 + - - +
273B ALA* 4.1 11.0 - - + +
275B CYS* 4.4 4.3 - - + -
279B TYR* 3.7 19.3 - - + -
287B MET* 3.6 39.7 - - + +
288B GLY* 1.3 81.0 - - - +
290B PRO* 1.3 70.8 - - + +
291B THR* 3.3 14.2 + - + +
302B ILE* 4.0 25.8 - - + -
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Residues in contact with PRO 290 (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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190B ASN* 4.6 16.2 - - - +
192B ILE* 3.9 14.8 - - + -
268B VAL* 4.4 16.4 - - + -
269B VAL 3.9 3.8 - - - +
270B PRO* 3.9 8.0 - - + -
279B TYR* 3.4 20.0 - - - +
289B VAL* 1.3 82.6 - - + +
291B THR* 1.3 60.6 + - - +
302B ILE* 3.6 3.5 - - - +
303B LEU* 2.9 51.8 + - + +
305B LEU* 4.1 17.0 - - + -
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Residues in contact with THR 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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268B VAL* 3.2 8.5 - - - +
269B VAL 2.6 44.8 + - - -
271B CYS* 3.6 19.0 - - - -
273B ALA* 3.7 20.6 - - + -
289B VAL* 3.5 20.2 - - + +
290B PRO* 1.3 74.9 - - - +
292B ILE* 1.3 65.1 + - - +
293B ILE* 3.5 18.9 - - - +
298B VAL* 3.9 14.8 - - + -
301B ASP 3.2 12.1 - - - +
302B ILE* 4.3 2.2 - - + -
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Residues in contact with ILE 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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266B LYS* 3.7 34.5 - - + +
267B ALA 3.3 3.4 - - - +
268B VAL* 3.7 26.2 - - + +
291B THR* 1.3 79.2 - - - +
293B ILE* 1.3 58.6 + - - +
298B VAL* 3.6 2.6 - - - -
299B GLU* 2.8 42.0 + - + +
301B ASP* 2.9 34.5 + - + +
303B LEU* 4.1 21.3 - - + -
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 4.4 14.8 - - + -
257B MET* 4.2 22.0 - - + +
260B ALA* 3.7 26.3 - - + +
261B TYR* 3.8 17.3 - - + +
266B LYS* 3.1 7.0 + - - -
267B ALA 2.9 31.2 + - - +
269B VAL* 3.6 31.6 - - + -
271B CYS* 4.3 5.4 - - - -
291B THR* 3.5 16.4 - - - +
292B ILE* 1.3 74.8 - - - +
294B GLY* 1.3 65.0 + - - +
297B GLY 3.4 13.0 - - - +
298B VAL* 4.5 8.7 - - + -
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Residues in contact with GLY 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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260B ALA 3.7 7.6 - - - -
261B TYR* 3.2 20.8 - - - -
264B ASP* 3.5 10.8 - - - -
266B LYS 4.2 3.1 - - - -
293B ILE* 1.3 74.1 - - - +
295B LYS* 1.3 60.8 + - - -
296B ASN 3.2 3.6 - - - -
297B GLY 2.9 23.5 + - - +
299B GLU* 3.2 13.7 + - - -
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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