Contacts of the strand formed by residues 380 - 384 (chain A) in PDB entry 2P6U
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 GLU 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A VAL* 3.6 4.9 - - + +
216A LEU* 4.1 6.2 - - - +
218A LEU* 2.8 49.2 - - + +
227A ARG* 4.7 1.7 + - - -
341A ARG* 3.5 13.3 + - + +
342A ARG* 3.3 47.0 + - - -
343A VAL 3.1 23.4 + - - -
370A ALA* 3.4 7.4 - - - +
379A GLY* 1.3 74.1 - - - -
381A ALA* 1.3 58.8 + - - +
382A ILE* 3.9 15.0 - - + -
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Residues in contact with ALA 381 (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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206A LEU* 3.8 13.9 - - + -
207A VAL 3.1 7.9 + - - +
208A GLU* 3.5 6.0 - - + +
209A GLY 2.9 25.5 + - - +
343A VAL* 3.3 9.6 - - + +
345A VAL* 6.2 1.3 - - + -
363A TYR* 4.5 5.3 + - + +
367A ALA* 3.6 39.0 - - + +
370A ALA* 4.2 1.1 - - + -
380A GLU* 1.3 75.3 - - - +
382A ILE* 1.3 62.2 + - - +
383A ILE* 4.1 1.2 + - - +
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Residues in contact with ILE 382 (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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209A GLY* 2.8 14.4 - - - +
211A LEU* 3.5 33.4 - - + +
216A LEU* 3.5 23.1 - - + -
234A LEU* 4.5 5.2 - - + -
342A ARG* 4.3 17.0 - - + +
343A VAL 3.0 7.3 + - - +
344A ILE* 3.7 24.1 - - + +
345A VAL* 2.8 29.7 + - - +
380A GLU* 3.9 29.2 - - + -
381A ALA* 1.3 80.7 - - - +
383A ILE* 1.3 65.7 + - - +
384A ILE* 3.5 6.9 + - + +
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Residues in contact with ILE 383 (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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209A GLY 2.9 11.0 + - - +
210A VAL* 3.2 22.7 - - + +
211A LEU 3.2 4.7 + - - -
345A VAL* 3.8 12.8 - - + +
347A SER 5.4 0.2 - - - +
348A LEU* 3.6 26.7 - - + -
363A TYR* 3.2 55.4 - - + +
382A ILE* 1.3 71.9 - - - +
384A ILE* 1.3 58.8 + - - +
385A VAL* 3.1 27.0 + - + -
393A ALA* 4.2 9.6 - - + +
397A TYR* 3.9 18.2 - - + -
398A ILE* 4.3 5.4 - - + -
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Residues in contact with ILE 384 (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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211A LEU* 3.7 37.7 - - + +
231A PHE* 4.0 33.9 - - + -
344A ILE* 3.5 34.1 - - + -
345A VAL 3.0 7.6 + - - +
346A ARG* 2.6 44.4 - - - +
347A SER* 4.4 3.6 - - - -
348A LEU* 5.2 0.9 + - - +
382A ILE* 4.2 5.2 - - + -
383A ILE* 1.3 70.2 - - - +
385A VAL* 1.3 65.1 + - - +
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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