Contacts of the strand formed by residues 271 - 277 (chain B) in PDB entry 3CL1
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 ARG 271 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B ARG* 5.6 2.4 - - - +
269B GLY 3.6 1.0 - - - -
270B ASP* 1.3 112.0 + - - +
272B MET* 1.3 61.1 + - - +
273B PHE* 3.4 34.3 - - + -
297B GLY 3.8 0.7 - - - +
301B LEU* 3.6 7.9 - - - +
307B ARG* 2.7 36.3 + - - +
321B SER* 4.2 13.7 + - - -
322B LEU 3.1 20.6 - - - +
323B HIS* 3.4 30.0 + - + +
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Residues in contact with MET 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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271B ARG* 1.3 74.7 - - - +
273B PHE* 1.3 65.3 + - - +
274B PHE* 3.8 11.7 - - + -
295B PHE* 3.6 41.7 - - + -
296B PHE 3.4 21.8 - - - +
297B GLY 3.9 7.2 - - - -
298B GLU* 3.8 11.2 - - + -
301B LEU* 3.6 15.5 - - + +
321B SER* 3.2 4.9 - - - -
322B LEU* 2.7 49.3 + - + +
327B PHE* 3.9 21.8 - - + -
341B PHE* 3.8 18.2 - - + -
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Residues in contact with PHE 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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254B ARG* 3.8 27.1 - - - -
262B ILE* 3.8 17.0 - - + -
263B CYS* 4.7 5.4 - - + -
271B ARG* 3.4 36.3 - - + -
272B MET* 1.3 78.5 - - - +
274B PHE* 1.3 64.8 + - - +
295B PHE* 3.1 9.1 - - - +
296B PHE* 2.8 75.8 + + + +
297B GLY* 4.8 0.4 - - - -
307B ARG* 3.9 12.3 - - - -
319B LEU* 3.9 20.6 - - + -
320B LEU 3.3 4.9 - - - +
321B SER* 3.5 25.6 - - - -
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Residues in contact with PHE 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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233B VAL* 3.9 29.4 - - + -
235B LEU* 3.9 6.7 - - + -
236B PHE* 3.6 31.6 - + - -
251B LEU* 4.0 22.0 - - + -
272B MET* 3.8 14.6 - - + -
273B PHE* 1.3 72.6 - - - +
275B VAL* 1.3 62.9 - - - +
276B VAL 3.7 0.3 + - - -
294B ALA 3.5 4.7 - - - +
295B PHE* 3.6 20.9 - + + -
319B LEU* 3.4 7.6 - - - +
320B LEU* 2.7 47.5 + - + +
322B LEU* 4.0 22.4 - - + -
330B LEU* 4.8 0.2 - - + -
341B PHE* 3.8 31.4 - + - -
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Residues in contact with VAL 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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233B VAL* 4.1 4.9 - - - +
274B PHE* 1.3 71.8 - - - +
276B VAL* 1.3 59.8 + - - +
277B GLU 4.0 9.2 - - - +
278B GLY 3.4 28.3 - - - +
279B SER* 4.4 1.6 - - - -
280B VAL* 4.2 8.1 - - + -
290B LEU 4.1 11.0 - - - +
291B GLY 3.3 24.7 - - - +
292B PRO* 3.7 2.0 - - + -
293B GLY* 2.6 31.0 + - - -
294B ALA* 2.8 19.8 + - + +
296B PHE* 3.9 27.1 - - + -
317B VAL* 4.6 3.4 - - + -
318B SER 3.9 4.0 - - - +
319B LEU* 4.1 6.1 - - + -
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Residues in contact with VAL 276 (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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229B LEU* 3.7 37.0 - - + +
232B ALA* 3.6 28.9 - - + +
233B VAL* 4.4 2.5 - - + -
274B PHE 4.4 0.4 - - - +
275B VAL* 1.3 76.1 - - - +
277B GLU* 1.3 63.8 + - + +
292B PRO* 3.3 17.6 - - - +
318B SER* 2.8 26.9 + - - +
319B LEU 4.4 0.4 - - - -
320B LEU* 3.6 42.4 - - + +
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Residues in contact with GLU 277 (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 VAL* 4.0 1.3 - - - +
276B VAL* 1.3 83.2 - - + +
278B GLY* 1.3 66.8 + - - +
292B PRO* 4.3 5.8 - - + -
316B THR 4.7 0.7 - - - -
317B VAL* 3.5 3.5 - - - +
318B SER* 2.8 44.1 + - - +
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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