Contacts of the strand formed by residues 528 - 535 (chain C) in PDB entry 3HN8
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 528 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459C MET* 3.2 33.7 - - + +
519C VAL* 3.7 2.9 - - - -
520C ASP* 2.9 41.5 + - - +
522C ASP* 3.1 15.4 - - - +
526C HIS 4.5 3.6 - - - +
527C ASN* 1.3 73.8 - - - +
529C VAL* 1.3 64.1 + - - +
530C ILE* 4.4 0.2 - - - +
602C CA 3.0 20.3 - - - -
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Residues in contact with VAL 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C MET* 4.1 12.0 - - - +
470C LYS* 5.7 4.9 - - - +
517C ALA* 4.7 5.8 - - + -
518C VAL 3.7 6.3 - - - +
519C VAL* 3.9 21.1 - - + -
527C ASN 5.4 2.0 - - - +
528C GLU* 1.3 74.9 - - - +
530C ILE* 1.3 64.1 + - - +
531C GLY* 3.6 23.6 - - - +
532C VAL* 4.2 12.6 - - + -
568C GLU* 5.3 15.0 - - + +
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Residues in contact with ILE 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C LEU* 3.4 46.4 - - - +
456C LEU* 4.2 13.2 - - + -
457C LYS* 3.8 21.8 - - + +
459C MET* 3.4 23.6 - - + +
465C SER* 3.9 27.8 - - - -
467C PRO* 4.6 2.0 - - + -
518C VAL* 2.9 31.6 + - + +
519C VAL 4.3 0.4 - - - -
520C ASP* 3.7 19.1 - - - +
528C GLU 3.6 0.2 + - - -
529C VAL* 1.3 76.0 - - - +
531C GLY* 1.3 61.3 + - - +
565C LEU* 4.9 1.3 - - + -
567C GLU* 5.4 1.2 - - - +
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Residues in contact with GLY 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C LEU* 4.0 8.3 - - - -
517C ALA* 3.3 4.3 - - - +
518C VAL 2.9 26.3 + - - +
529C VAL* 3.6 2.7 - - - +
530C ILE* 1.3 82.9 - - - +
532C VAL* 1.3 66.3 + - - +
565C LEU* 4.0 18.3 - - - +
566C VAL 3.9 8.1 - - - -
567C GLU* 5.7 0.4 - - - -
568C GLU 5.8 0.4 - - - -
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Residues in contact with VAL 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C SER* 3.6 20.4 - - - +
516C ILE 3.1 14.1 - - - +
517C ALA* 3.8 12.6 - - + +
529C VAL* 4.2 7.4 - - + -
531C GLY* 1.3 80.6 - - - +
533C CYS* 1.3 76.0 + - - +
534C ARG* 3.8 18.2 - - - +
564C GLN 3.7 0.7 - - - +
565C LEU* 3.2 6.7 - - - +
566C VAL* 2.7 41.8 + - - +
568C GLU* 4.1 35.0 - - + +
571C LEU* 5.2 4.0 - - + -
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Residues in contact with CYS 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433C LEU* 4.2 8.5 - - - -
435C PHE* 4.0 21.3 - - - -
515C SER* 3.7 1.7 - - - -
516C ILE* 2.8 58.6 + - - +
532C VAL* 1.3 77.9 - - - +
534C ARG* 1.3 67.7 + - - +
563C HIS* 4.1 17.9 - - + +
564C GLN 3.8 14.6 - - - +
565C LEU* 4.3 6.7 - - + -
566C VAL* 5.4 2.7 - - - -
571C LEU* 6.2 1.6 - - - -
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Residues in contact with ARG 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C ILE* 4.2 8.6 - - + +
514C LEU 4.0 5.4 - - - +
515C SER* 3.9 19.3 + - - -
532C VAL* 3.8 17.6 - - - +
533C CYS* 1.3 81.7 - - - +
535C VAL* 1.3 65.9 + - - +
538C GLU 5.2 3.4 - - - +
539C ALA* 4.2 23.8 - - + -
540C ALA* 5.0 4.7 - - + +
541C ASP 6.1 0.4 - - - +
544C GLY* 3.8 14.4 - - - -
563C HIS* 4.7 4.7 + - - -
568C GLU* 4.0 11.1 + - - -
571C LEU* 3.3 52.8 - - + +
572C SER* 4.2 1.8 - - - +
573C SER* 3.2 36.0 + - - +
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Residues in contact with VAL 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C PHE* 4.6 14.1 - - + -
437C LEU* 4.2 7.0 - - + -
513C GLY* 3.6 0.7 - - - -
514C LEU* 2.9 61.9 + - + +
516C ILE* 5.0 2.2 - - + -
533C CYS 5.5 0.2 - - - +
534C ARG* 1.3 77.2 - - - +
536C GLY* 1.3 59.5 + - - +
537C PRO 5.2 0.2 - - - -
539C ALA* 4.6 1.1 - - - -
544C GLY 2.9 24.5 - - - +
547C HIS* 3.6 31.2 - - + +
548C TRP* 3.7 10.6 - - + +
563C HIS* 4.2 4.9 - - - +
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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