Contacts of the strand formed by residues 275 - 280 (chain B) in PDB entry 4ISO
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 CYS 275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B TRP* 3.8 13.3 - - + -
267B TYR 3.3 3.8 - - - -
268B TYR* 3.9 13.5 - - - -
274B ILE* 1.3 81.0 - - - +
276B LYS* 1.3 64.8 + - - +
293B GLU* 4.1 25.3 + - + +
296B CYS* 2.1 65.7 - - + -
297B ILE* 3.4 14.4 - - + +
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Residues in contact with LYS 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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266B TRP* 3.2 10.6 - - - -
267B TYR* 2.8 64.2 + - + +
269B ASP* 3.3 31.2 + - + -
272B GLU* 2.7 26.8 + - - +
274B ILE* 3.8 15.0 - - + -
275B CYS* 1.3 78.3 - - - +
277B SER* 1.3 64.0 + - - +
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PRO* 6.5 0.9 - - - -
265B ARG 3.3 9.6 - - - -
266B TRP* 3.6 24.1 - - - -
267B TYR* 3.8 6.8 - - - -
276B LYS* 1.3 76.6 - - - +
278B PHE* 1.3 64.7 + - - +
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Residues in contact with PHE 278 (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 ASN* 3.6 24.7 - - + +
255B LYS 3.5 30.7 - - - -
256B VAL* 4.4 3.6 - - + -
264B PRO* 3.7 3.1 - - - +
265B ARG* 2.9 56.7 + - + +
266B TRP 3.7 14.1 - - - -
267B TYR* 3.7 31.2 - + + -
277B SER* 1.3 76.8 - - - +
279B VAL* 1.3 80.3 + - - +
280B TYR* 4.0 11.4 - - + -
288B ASN 4.1 5.4 - - - -
289B ASN* 3.7 27.8 - - + -
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Residues in contact with VAL 279 (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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143A HIS* 3.6 35.3 - - + +
148A GLY 5.7 0.7 - - - +
192A GLN* 4.5 4.6 - - + +
256B VAL* 3.4 28.5 - - - +
262B SER* 3.4 39.7 - - - -
263B PHE 3.5 2.0 - - - +
264B PRO* 4.7 10.8 - - + -
278B PHE* 1.3 83.2 - - - +
280B TYR* 1.3 61.1 + - - +
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Residues in contact with TYR 280 (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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303A GOL 3.5 17.0 + - - -
255B LYS 3.4 16.8 - - - -
256B VAL* 3.5 4.5 - - - -
261B GLY 3.5 3.5 - - - +
263B PHE* 2.8 45.7 + - + +
265B ARG* 3.6 26.9 - - + -
278B PHE* 4.0 9.4 + - + -
279B VAL* 1.3 73.2 - - - +
281B GLY* 1.3 67.4 + - - +
282B GLY* 3.3 31.7 + - - -
283B CYS* 3.1 20.3 + - - -
284B LEU 3.3 1.6 + - - -
285B GLY* 3.0 41.1 + - - -
289B ASN* 3.5 20.0 - - - +
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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