Contacts of the strand formed by residues 375 - 378 (chain B) in PDB entry 3N9Y
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 LEU 375 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B VAL* 3.9 12.6 - - + -
58B GLU 3.8 12.3 + - - +
59B SER* 3.3 23.1 - - - +
60B VAL 2.9 24.3 + - - -
82B PHE* 3.7 31.9 - - + +
356B GLN* 3.8 22.9 - - + -
357B ARG 3.8 11.2 - - - +
358B TYR* 3.7 35.8 - - + +
373B LYS 3.6 2.4 + - - -
374B THR* 1.3 77.8 - - - +
376B VAL* 1.3 62.3 + - - +
377B GLN* 3.9 12.1 - - + +
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 3.3 23.3 - - + +
62B VAL* 4.4 18.2 - - + -
71B LEU* 3.8 31.8 - - + +
356B GLN* 3.1 3.3 - - - +
357B ARG 2.9 37.6 + - - +
359B LEU* 4.0 31.4 - - + -
365B LEU* 4.7 6.1 - - + -
370B ILE* 4.4 11.0 - - + -
374B THR 4.2 0.7 - - - +
375B LEU* 1.3 77.7 - - - +
377B GLN* 1.3 69.7 + - - +
378B VAL 4.4 0.2 + - - -
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Residues in contact with GLN 377 (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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39B HIS* 5.4 0.2 - - - -
57B VAL* 5.6 1.4 - - - +
59B SER* 2.8 32.1 + - - +
60B VAL 2.8 9.1 + - - +
61B TYR* 3.4 35.1 + - + +
62B VAL* 2.9 27.4 + - - +
82B PHE* 5.4 3.8 - - - -
354B THR* 3.0 30.0 + - - +
355B LEU 3.1 6.5 - - - +
356B GLN* 3.5 18.9 - - + +
375B LEU* 3.9 11.0 - - + +
376B VAL* 1.3 77.0 - - - +
378B VAL* 1.3 63.5 + - - +
379B ALA 3.8 0.5 + - - -
602B CLR 4.3 13.3 + - - -
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Residues in contact with VAL 378 (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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62B VAL* 3.5 17.9 - - + +
63B ILE 5.4 0.7 - - - +
68B VAL* 3.6 35.7 - - + -
71B LEU* 3.7 28.3 - - + -
72B PHE* 4.3 6.7 - - + -
354B THR* 3.1 4.7 - - - -
355B LEU* 2.7 39.7 + - + +
377B GLN* 1.3 72.5 - - - +
379B ALA* 1.3 61.1 + - - +
380B ILE* 2.9 28.9 + - + +
383B LEU* 4.8 4.7 - - + -
414B LEU* 4.3 5.8 - - + -
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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