Contacts of the strand formed by residues 380 - 385 (chain B) in PDB entry 2AX1
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 380 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B GLU* 5.2 0.4 + - - -
372B VAL* 3.6 34.7 - - + +
373B ALA 3.6 3.4 - - - -
374B HIS* 3.8 18.8 + - + -
378B GLY 3.7 2.4 + - - -
379B LYS* 1.3 89.3 - - + +
381B VAL* 1.3 61.0 + - - +
382B TYR* 2.9 43.8 + - + -
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Residues in contact with VAL 381 (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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372B VAL* 3.6 3.9 - - - +
373B ALA* 2.8 34.0 + - - +
375B ASP* 4.0 16.2 - - + +
379B LYS* 3.6 14.1 - - + +
380B ARG* 1.3 79.7 - - - +
382B TYR* 1.3 74.0 + - - +
383B TYR* 3.9 5.1 + - + -
467B HIS 6.1 0.2 - - - +
470B SER* 4.1 16.2 - - - +
474B LEU* 3.8 36.6 - - + -
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Residues in contact with TYR 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 3.5 28.5 - - + +
205B VAL* 4.0 28.9 - - + -
209B LYS* 4.2 20.2 + - - -
360B LEU* 6.1 1.6 - - + -
361B GLU* 4.7 2.9 - - + -
370B VAL* 3.9 17.3 - - + -
371B SER 3.5 2.0 - - - +
372B VAL* 3.4 28.7 - - + -
380B ARG* 2.9 36.4 + - + -
381B VAL* 1.3 83.7 - - - +
383B TYR* 1.3 62.1 + - - +
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Residues in contact with TYR 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 4.0 12.7 - - - +
370B VAL* 3.6 2.6 - - - -
371B SER* 3.1 59.1 + - - -
372B VAL 3.9 2.8 + - - -
373B ALA* 3.9 22.4 - - + -
381B VAL* 3.9 11.2 - - + -
382B TYR* 1.3 75.8 - - - +
384B LEU* 1.3 71.4 + - - +
385B THR* 3.7 20.6 + - - -
417B PRO* 3.9 30.3 - - + -
418B THR* 3.8 19.9 - - + -
474B LEU* 4.5 6.5 - - + -
477B TYR* 3.3 23.3 - + - -
481B GLU* 3.5 21.5 + - - +
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Residues in contact with LEU 384 (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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197B PRO* 4.7 17.9 + - + +
200B ARG* 3.8 23.1 - - + +
201B VAL* 4.7 9.3 - - + +
204B LEU* 4.8 5.8 - - + -
368B SER* 3.6 22.0 - - - -
369B ASN* 3.7 19.5 - - - +
370B VAL* 4.3 14.6 - - + -
383B TYR* 1.3 76.1 - - - +
385B THR* 1.3 59.2 + - - +
414B MET 5.0 1.8 - - - +
415B TYR* 3.4 18.4 - - + -
417B PRO* 5.3 3.0 - - - +
418B THR* 3.4 10.9 - - - +
1002B 5EE 3.7 42.6 - - + -
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Residues in contact with THR 385 (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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368B SER* 3.2 8.3 - - - -
369B ASN* 2.9 47.5 + - - +
371B SER* 4.1 11.7 - - - -
383B TYR* 3.7 6.1 - - - -
384B LEU* 1.3 75.2 - - - +
386B ARG* 1.3 67.8 + - - +
415B TYR* 3.8 10.1 - - - -
418B THR* 3.3 9.2 - - - +
420B TRP* 3.0 13.7 + - - -
481B GLU* 2.7 31.5 + - - +
484B ARG* 3.4 17.9 - - - +
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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
------------------------------------------------------------
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