Contacts of the strand formed by residues 380 - 385 (chain A) in PDB entry 2LB2
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A ARG 4.3 0.7 - - - +
375A LYS* 5.4 0.4 - - - -
376A ASP* 3.4 29.0 + - - +
378A LYS* 2.9 30.7 + - + +
379A GLY* 1.3 90.1 + - - +
381A THR* 1.3 60.1 + - - +
382A TYR* 4.3 1.7 + - - +
393A TRP* 3.3 36.2 - - + -
178B GLU* 2.7 53.4 + - - +
179B TPO 2.6 68.2 + - - +
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Residues in contact with THR 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 4.2 4.2 + - - -
374A ARG 3.5 7.2 + - - -
375A LYS* 3.4 54.1 + - + +
380A ARG* 1.3 72.1 - - - +
382A TYR* 1.3 63.3 + - - +
383A TYR* 4.4 18.8 - - + +
393A TRP* 3.0 22.6 - - - +
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Residues in contact with TYR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLU 4.2 0.2 - - - +
373A GLU* 3.6 2.9 - - - +
374A ARG* 2.8 63.2 + - + -
376A ASP* 6.2 1.8 - - + -
380A ARG 5.4 1.8 - - - -
381A THR* 1.3 78.6 + - - +
383A TYR* 1.3 67.4 + - - +
384A VAL* 3.7 15.1 - - + +
391A THR* 2.9 31.4 - - - -
392A THR 3.4 10.3 - - - +
393A TRP* 3.3 22.9 - + + -
181B PRO* 4.1 0.9 - - + -
182B PRO* 3.1 35.8 - - + +
183B GLY 3.3 12.1 + - - -
186B SER 3.7 0.9 + - - -
187B GLU* 2.6 30.7 + - - -
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Residues in contact with TYR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 3.6 25.1 - - + -
371A TRP* 3.4 24.1 - - + -
372A GLU 3.6 5.6 - - - +
373A GLU* 3.4 30.6 + - + -
375A LYS* 5.4 2.1 - - - -
381A THR* 4.4 22.1 - - + +
382A TYR* 1.3 76.5 - - - +
384A VAL* 1.3 61.5 + - - +
390A THR 3.7 1.9 - - - +
391A THR* 3.8 0.2 - - - -
392A THR* 3.0 37.4 + - - +
393A TRP 4.0 9.9 - - - -
394A THR 3.3 24.7 - - - -
395A ARG* 2.8 44.4 + - - -
396A PRO* 3.9 11.0 - - + -
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A TRP* 3.0 12.4 - - - -
372A GLU* 2.9 23.2 + - + +
382A TYR* 3.7 20.6 - - + +
383A TYR* 1.3 70.9 - - - +
385A ASN* 1.3 61.2 + - - +
386A HIS* 2.9 25.7 - - - -
390A THR 3.1 13.5 - - - +
391A THR* 3.9 1.3 - - - -
184B TYR* 3.4 18.2 - - + -
185B LEU* 3.1 29.6 - - + +
187B GLU* 3.3 33.0 - - + +
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Residues in contact with ASN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A GLY 3.8 1.8 + - - -
371A TRP* 2.8 57.8 - - + +
384A VAL* 1.3 71.5 - - - +
386A HIS* 1.3 64.4 + - - +
387A ASN* 3.1 22.4 - - - +
388A ASN* 2.9 36.3 + - - +
389A ARG 2.8 23.4 + - - -
390A THR* 2.9 21.1 + - - -
398A MET* 5.4 1.6 - - - +
184B TYR* 2.8 11.8 - - - -
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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