Contacts of the strand formed by residues 581 - 586 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E TYR* 3.4 20.1 - - + +
525E PHE* 3.7 31.9 - - + -
536E ILE* 3.2 15.5 - - + +
538E GLN 4.9 1.1 - - - +
573E LEU* 4.0 20.4 - - + -
576E LYS* 3.1 34.0 + - + +
577E ARG* 3.4 17.1 - - - +
580E TYR* 1.3 84.6 + - + +
582E VAL* 1.3 60.9 + - - +
583E GLY 3.7 17.9 - - - +
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Residues in contact with VAL 582 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E SER 3.5 24.5 - - - +
335E GLN* 4.0 0.9 - - - -
336E PHE* 3.8 35.2 - - + +
343E PHE 3.8 6.0 - - - +
344E TYR* 3.4 14.9 - - - -
345E PHE* 3.0 24.2 + - + -
498E VAL* 4.7 3.6 - - + -
535E PRO* 3.8 19.7 - - + -
536E ILE 2.8 16.1 + - - +
537E ILE* 3.7 17.3 - - + -
580E TYR 3.8 5.4 - - - +
581E VAL* 1.3 76.1 - - - +
583E GLY* 1.3 56.6 + - - +
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Residues in contact with GLY 583 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E TYR* 3.4 10.0 - - - -
345E PHE* 3.2 20.9 - - - -
536E ILE 3.8 1.6 + - - -
537E ILE* 3.5 12.3 - - - +
538E GLN* 3.0 22.0 + - - +
581E VAL* 3.6 9.4 - - - +
582E VAL* 1.3 82.6 - - - +
584E GLU* 1.3 62.5 + - - +
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Residues in contact with GLU 584 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E TYR* 2.6 29.9 + - + +
345E PHE* 2.9 13.8 + - - +
346E HIS* 4.4 5.6 - - - -
347E GLY 3.0 25.3 + - - +
538E GLN* 3.3 7.9 - - + +
541E TYR* 4.2 8.3 + - + -
570E HIS* 4.0 4.9 - - - -
573E LEU* 3.4 28.4 - - + +
583E GLY* 1.3 73.8 - - - +
585E LEU* 1.3 63.6 + - - +
586E ILE 4.2 0.4 - - - -
625E ARG* 2.9 41.9 + - - -
626E TYR* 3.7 17.8 - - - +
629E ILE* 4.6 1.6 - - - -
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Residues in contact with LEU 585 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345E PHE* 4.4 14.4 - - + -
347E GLY* 3.4 24.5 - - - +
348E VAL 3.7 9.2 - - - +
349E ASN* 3.6 8.1 - - - +
380E ALA* 4.4 10.3 - - + +
381E PHE* 4.7 0.9 - - - -
382E ARG* 3.9 29.2 - - + +
404E ILE* 4.1 19.1 - - + -
537E ILE* 4.5 7.2 - - + -
538E GLN 2.8 10.0 + - - +
539E SER* 3.2 45.2 - - - +
540E GLU* 3.5 5.9 + - - -
541E TYR* 3.8 6.4 - - - -
584E GLU* 1.3 81.9 - - - +
586E ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 586 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347E GLY 3.2 4.8 + - - +
348E VAL* 3.7 22.2 - - + -
349E ASN* 2.9 26.8 + - - -
541E TYR* 3.7 27.4 - - + +
542E GLY* 5.2 0.7 - - - -
562E GLN* 5.5 0.9 - - - +
566E LEU* 3.6 34.1 - - + -
585E LEU* 1.3 72.5 - - - +
587E TRP* 1.3 73.4 + - - +
588E ASN* 3.8 6.9 - - - +
608E ILE* 3.4 31.9 - - + -
622E LEU* 3.6 26.9 - - + -
626E TYR* 4.1 1.6 + - - +
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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