Contacts of the strand formed by residues 581 - 586 (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 VAL 581 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A TYR* 3.3 25.5 - - + +
525A PHE* 3.7 32.3 - - + -
536A ILE* 3.2 14.1 - - + +
538A GLN 5.0 0.9 - - - +
573A LEU* 4.1 14.6 - - + -
576A LYS* 3.0 35.6 + - + +
577A ARG* 3.4 17.1 - - + +
579A LYS 5.2 0.2 + - - -
580A TYR* 1.3 84.5 - - + +
582A VAL* 1.3 60.6 + - - +
583A GLY 3.7 18.6 - - - +
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Residues in contact with VAL 582 (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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334A SER 3.5 24.5 - - - +
335A GLN* 3.9 0.9 - - - -
336A PHE* 3.8 31.9 - - + +
343A PHE 3.8 5.1 - - - +
344A TYR* 3.3 15.2 - - - -
345A PHE* 3.0 25.6 + - - -
498A VAL* 4.5 4.9 - - + -
535A PRO* 3.7 26.0 - - + -
536A ILE 2.8 12.7 + - - +
537A ILE* 3.7 22.9 - - + -
580A TYR 4.1 0.7 - - - +
581A VAL* 1.3 75.4 - - - +
583A GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 583 (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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344A TYR* 3.4 9.6 - - - -
345A PHE* 3.2 20.9 - - - -
536A ILE 3.8 3.0 + - - -
537A ILE* 3.5 14.4 - - - -
538A GLN* 3.0 22.2 + - - +
581A VAL* 3.6 9.9 - - - +
582A VAL* 1.3 81.0 - - - +
584A GLU* 1.3 62.3 + - - +
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Residues in contact with GLU 584 (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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344A TYR* 2.7 30.1 + - + +
345A PHE* 2.9 15.0 + - - +
346A HIS* 4.3 4.9 - - - -
347A GLY 3.0 24.4 + - - +
538A GLN* 3.3 8.1 - - + +
541A TYR* 4.2 8.3 + - + -
570A HIS* 4.1 4.3 - - - -
573A LEU* 3.6 27.1 - - + +
583A GLY* 1.3 75.6 - - - +
585A LEU* 1.3 66.5 + - - +
586A ILE 4.2 0.2 - - - -
625A ARG* 2.9 42.6 + - - -
626A TYR* 3.6 18.8 - - - +
629A ILE* 4.5 1.6 - - - -
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Residues in contact with LEU 585 (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* 4.4 15.5 - - + -
347A GLY* 3.5 23.6 - - - +
348A VAL 3.8 11.7 - - - +
349A ASN* 3.4 7.4 + - - +
380A ALA* 4.4 10.3 - - + +
381A PHE* 4.8 1.1 - - - -
382A ARG* 4.0 26.9 - - + +
404A ILE* 4.1 18.4 - - + -
537A ILE* 4.4 9.4 - - + -
538A GLN 2.9 10.0 + - - +
539A SER* 3.2 42.7 - - - +
540A GLU* 3.6 4.3 - - - -
541A TYR* 3.8 7.3 - - - -
584A GLU* 1.3 82.1 - - - +
586A ILE* 1.3 63.1 + - - +
587A TRP 3.6 1.0 + - - -
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Residues in contact with ILE 586 (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 3.3 5.9 + - - +
348A VAL* 3.7 21.5 - - + -
349A ASN* 3.0 25.3 + - - -
541A TYR* 3.7 28.3 - - + +
542A GLY* 5.6 0.2 - - - -
562A GLN* 5.4 1.3 - - - +
566A LEU* 3.5 34.8 - - + -
585A LEU* 1.3 71.4 - - - +
587A TRP* 1.3 71.9 + - - +
588A ASN* 3.7 7.3 - - - +
608A ILE* 3.4 34.1 - - + -
622A LEU* 3.6 26.2 - - + -
626A TYR* 4.1 1.4 + - - +
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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