Contacts of the strand formed by residues 297 - 300 (chain B) in PDB entry 3H60
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 297 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B PHE* 4.6 1.8 - + - -
260B PRO* 3.6 39.3 - - + -
266B TYR* 3.6 23.1 - + + -
268B PHE* 3.7 13.5 - + - -
286B LEU* 3.3 41.5 - - + -
289B PHE* 3.7 20.9 - + + +
290B LYS* 2.9 51.8 + - + +
293B TYR* 3.0 16.9 + - + +
294B PRO 3.9 0.2 - - - +
295B ASP 3.7 0.8 - - - -
296B HIS* 1.3 82.7 - - - +
298B HIS* 1.3 60.3 + - - +
299B LEU* 3.7 19.7 - - + -
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Residues in contact with HIS 298 (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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223B LEU* 6.2 1.6 - - + -
227B VAL* 4.2 15.4 - - + +
229B THR* 4.2 12.1 + - + -
237B ILE* 4.3 9.3 - - + +
265B PRO* 5.5 0.2 - - + -
266B TYR 2.8 12.6 + - - +
267B ILE* 3.2 17.5 - - + +
268B PHE* 2.6 32.4 + - - -
290B LYS* 4.2 12.6 - - - +
294B PRO 4.6 1.4 + - - -
295B ASP* 3.7 26.8 + - - -
296B HIS* 4.0 9.4 - - - -
297B PHE* 1.3 78.8 + - - +
299B LEU* 1.3 65.0 + - - +
300B LEU* 5.1 0.7 - - + -
342B GLN* 3.3 42.6 + - - +
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Residues in contact with LEU 299 (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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220B LEU* 5.4 4.3 - - + +
268B PHE* 3.5 20.6 - - + -
272B PHE* 3.9 17.3 - - + -
283B ILE* 5.9 0.2 - - + -
286B LEU* 4.0 19.3 - - + +
287B PHE* 3.9 27.8 - - + -
290B LYS* 3.8 33.9 - - + +
297B PHE* 3.7 21.8 - - + -
298B HIS* 1.3 83.3 - - - +
300B LEU* 1.3 68.0 + - - +
338B LEU* 4.0 13.7 - - + +
339B PRO* 3.5 21.7 - - - +
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Residues in contact with LEU 300 (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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227B VAL* 5.1 2.2 - - + -
267B ILE* 4.1 15.7 - - + -
268B PHE 2.9 9.6 + - - +
269B ASN* 3.3 27.8 - - - +
270B GLY* 3.0 23.3 + - - +
272B PHE* 3.2 7.4 - - - -
298B HIS* 5.1 0.7 - - + -
299B LEU* 1.3 82.9 - - - +
301B ARG* 1.3 63.0 + - - +
338B LEU* 4.5 2.0 - - - -
339B PRO* 3.6 18.6 - - + +
340B LEU 4.8 3.8 - - - +
341B ALA* 4.2 10.8 - - - +
342B GLN* 3.8 30.1 - - + +
350B ILE* 3.5 35.4 - - + +
351B MET* 4.4 0.9 - - - +
352B HIS 5.4 0.7 - - - +
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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