Contacts of the strand formed by residues 345 - 349 (chain A) in PDB entry 3HN3
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 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A PHE* 3.9 39.7 - + + -
343A PHE* 3.7 25.8 - + - -
344A TYR* 1.3 78.2 - - - +
346A HIS* 1.3 58.9 + - - +
379A ASN* 3.8 4.0 - - - -
380A ALA* 3.6 19.5 - - + -
402A VAL* 4.0 4.3 - - + -
404A ILE* 4.0 31.4 - - + -
444A VAL* 3.9 15.5 - - + -
445A MET* 4.8 0.9 - - + -
537A ILE* 3.9 22.2 - - + -
582A VAL* 3.0 20.5 + - + -
583A GLY* 3.2 10.8 - - - -
584A GLU 2.9 26.9 + - - +
585A LEU* 4.4 13.0 - - + -
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Residues in contact with HIS 346 (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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292A LEU* 4.4 6.5 - - + +
344A TYR* 3.6 17.9 - + + -
345A PHE* 1.3 71.5 - - - +
347A GLY* 1.3 57.2 + - - +
377A GLY 2.8 24.1 + - - -
378A ALA* 3.3 5.5 - - - -
379A ASN* 2.8 54.5 + - + -
584A GLU* 3.6 4.5 - - + -
626A TYR* 3.3 41.5 - + + -
629A ILE* 3.7 26.7 - - + -
630A ALA* 4.2 20.8 - - + +
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Residues in contact with GLY 347 (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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345A PHE 3.9 0.4 - - - -
346A HIS* 1.3 75.1 - - - +
348A VAL* 1.3 69.5 + - - +
378A ALA* 4.2 4.9 - - - -
380A ALA 3.2 15.9 - - - -
584A GLU 3.0 9.9 + - - -
585A LEU* 3.8 11.4 - - - -
586A ILE* 3.3 10.0 + - - +
626A TYR* 2.6 26.1 + - - -
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Residues in contact with VAL 348 (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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347A GLY* 1.3 81.3 - - - +
349A ASN* 1.3 73.8 - - - +
350A LYS* 3.8 8.7 - - + -
373A LEU* 3.7 23.8 - - + -
376A LEU* 3.7 31.0 - - + -
378A ALA* 4.5 2.0 - - + -
380A ALA 3.1 3.8 + - - +
381A PHE* 3.1 35.7 - - + +
382A ARG 3.2 3.8 + - - -
585A LEU* 3.8 6.6 - - - +
586A ILE* 3.7 23.1 - - + +
589A PHE* 4.0 13.7 - - + +
608A ILE* 4.8 0.4 - - + -
626A TYR* 4.9 0.2 - - + -
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Residues in contact with ASN 349 (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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348A VAL* 1.3 75.0 - - - +
350A LYS* 1.3 61.8 + - - +
382A ARG* 2.9 41.7 + - - +
384A SER* 3.5 7.6 + - - +
539A SER 2.7 24.8 + - - +
540A GLU* 4.0 0.4 - - - +
585A LEU* 3.4 9.9 + - - +
586A ILE 3.0 26.9 + - - +
587A TRP* 3.3 33.2 - - + +
588A ASN* 3.3 3.2 - - - +
589A PHE* 2.9 30.1 + - - +
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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