Contacts of the strand formed by residues 356 - 360 (chain B) in PDB entry 2ADM
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 356 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B ILE* 3.8 13.5 - - + -
267B ARG 4.0 1.3 - - - -
268B PHE* 3.2 42.2 - + - -
331B LEU 3.9 0.3 - - - +
332B VAL* 3.4 10.2 - - - +
333B VAL* 2.8 46.8 + - + +
334B ALA 4.2 6.3 - - - -
335B HIS* 3.3 31.2 - + + -
355B GLU* 1.3 72.6 - - - +
357B HIS* 1.3 61.5 + - - +
358B LEU* 4.0 15.5 - - + -
395B LEU* 3.6 14.4 - - + -
396B THR* 4.0 4.3 - - - -
397B LEU* 3.9 31.2 - - + -
400B LEU* 3.8 18.6 - - + -
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Residues in contact with HIS 357 (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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265B HIS 3.4 1.9 - - - +
266B ILE 3.6 0.3 - - - -
267B ARG* 2.7 42.2 + - - +
269B ALA* 3.5 30.5 + - + -
325B PHE* 3.6 25.5 - + + -
326B TYR* 4.7 1.1 - + - -
330B HIS* 3.0 34.3 - + + -
331B LEU 3.8 1.6 - - - -
332B VAL* 3.7 15.1 - - + +
352B TRP* 3.3 28.9 - + + +
354B GLU 3.1 24.3 + - - -
355B GLU 3.6 9.2 + - - -
356B PHE* 1.3 73.6 - - - +
358B LEU* 1.3 62.3 + - - +
359B LEU* 3.9 1.5 + - - +
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Residues in contact with LEU 358 (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 LEU* 3.5 32.5 - - + -
264B PHE* 3.9 23.0 - - + -
265B HIS 3.3 4.3 - - - +
266B ILE* 4.1 11.7 - - + -
330B HIS* 3.4 21.4 + - - +
331B LEU* 3.0 42.7 + - + +
333B VAL* 4.0 16.2 - - + -
356B PHE* 4.0 17.9 - - + +
357B HIS* 1.3 86.8 - - - +
359B LEU* 1.3 62.5 + - - +
360B PRO* 4.0 4.2 - - - +
400B LEU* 4.1 10.3 - - + -
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Residues in contact with LEU 359 (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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264B PHE* 3.6 2.7 - - - -
265B HIS* 2.7 45.0 + - + +
267B ARG* 3.4 41.1 - - + +
324B ASP* 5.1 1.8 - - - +
325B PHE* 3.5 36.3 - - + -
328B THR* 4.8 13.5 - - + -
330B HIS* 4.0 23.1 - - + -
357B HIS 4.7 1.8 - - - +
358B LEU* 1.3 75.1 - - - +
360B PRO* 1.3 72.8 - - + +
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Residues in contact with PRO 360 (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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263B LEU 3.4 9.0 - - - +
264B PHE* 3.3 13.8 - - + -
265B HIS* 4.0 5.7 - - - -
330B HIS* 5.5 1.3 - - + -
345B TRP* 5.1 12.8 - - + -
358B LEU 4.0 3.4 - - - +
359B LEU* 1.3 91.4 - - + +
361B LYS* 1.3 63.3 + - - +
364B VAL* 4.2 14.8 - - + +
366B LEU* 4.0 24.5 - - + -
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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