Contacts of the strand formed by residues 522 - 529 (chain C) in PDB entry 2HYE
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 ASP 522 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509C LYS* 4.2 20.3 + - - +
520C PRO 4.0 1.4 + - - -
521C ILE* 1.3 70.3 - - - +
523C LEU* 1.3 62.1 + - - +
524C THR* 3.8 15.6 + - - -
25D LYS 3.2 15.7 + - - +
26D LYS* 3.4 26.1 + - - +
27D TRP 3.0 23.4 + - - -
28D ASN* 5.4 0.3 + - - -
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Residues in contact with LEU 523 (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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505C MET* 4.6 7.8 - - - +
508C PHE* 4.8 16.5 - - + -
509C LYS* 5.2 9.0 - - - +
521C ILE 3.4 7.4 + - - +
522C ASP* 1.3 76.7 + - - +
524C THR* 1.3 64.3 + - - +
525C VAL* 3.3 32.5 - - + -
550C LEU* 3.7 46.2 - - + +
551C GLN* 4.4 2.0 - - - +
554C PHE* 4.7 6.7 - - + -
27D TRP* 3.2 45.8 - - + +
29D ALA* 4.1 7.0 - - + -
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Residues in contact with THR 524 (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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505C MET* 4.0 20.0 - - + -
522C ASP* 3.8 13.4 + - - -
523C LEU* 1.3 73.6 + - - +
525C VAL* 1.3 70.2 + - - +
526C ASN* 5.5 3.8 - - - +
26D LYS* 6.1 1.0 - - - +
27D TRP 3.2 6.5 + - - +
28D ASN* 3.2 28.1 + - - +
29D ALA 3.0 23.4 + - - +
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Residues in contact with VAL 525 (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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501C SER* 4.1 3.3 - - - +
505C MET* 3.0 34.9 - - + +
523C LEU* 3.3 37.9 - - + -
524C THR* 1.3 77.7 - - - +
526C ASN* 1.3 82.0 + - - +
527C ILE* 4.8 2.0 - - + +
551C GLN* 6.5 0.2 - - - -
554C PHE* 3.7 36.8 - - + -
569C TRP* 4.3 14.4 - - + +
29D ALA* 3.5 15.7 - - + +
30D VAL* 4.9 0.2 - - - -
31D ALA* 5.0 3.4 - - + +
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Residues in contact with ASN 526 (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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461C LEU 4.7 0.7 - - - +
462C LEU* 3.6 19.1 - - + +
498C MET* 3.1 40.5 + - - +
501C SER* 3.1 24.8 - - - -
502C LYS* 5.1 1.2 - - - +
524C THR* 5.5 4.6 - - - +
525C VAL* 1.3 80.6 + - - +
527C ILE* 1.3 60.4 + - - +
528C LEU* 4.4 2.5 - - + -
29D ALA 3.0 13.2 + - - +
30D VAL* 3.4 6.0 - - + +
31D ALA 3.1 25.6 + - - +
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Residues in contact with ILE 527 (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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497C ASP* 3.8 16.5 - - - +
500C LEU* 5.4 3.4 - - + -
501C SER* 3.0 25.9 + - - +
504C ILE* 4.4 22.2 - - + -
525C VAL* 4.1 3.4 + - + -
526C ASN* 1.3 72.6 - - - +
528C LEU* 1.3 65.2 + - - +
554C PHE* 5.1 11.4 - - + -
558C TYR* 3.9 28.3 - - + +
567C LEU* 3.2 34.8 - - + -
31D ALA* 3.4 25.4 - - + +
33D TRP* 4.4 10.1 - - + +
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Residues in contact with LEU 528 (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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462C LEU* 3.8 16.6 - - + -
497C ASP* 4.0 4.5 - - + -
498C MET* 4.7 5.8 - - - -
526C ASN* 4.3 9.2 - - + +
527C ILE* 1.3 81.9 - - - +
529C THR* 1.3 59.8 + - - +
530C MET 3.2 1.7 + - - -
533C TRP* 3.3 58.6 - - + +
536C TYR* 5.9 0.2 - - + -
573C LEU* 4.8 2.9 - - + -
30D VAL* 3.5 26.5 - - + -
31D ALA 2.8 16.7 + - - +
32D LEU* 3.1 25.1 - - + -
33D TRP* 2.9 29.7 + - - -
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Residues in contact with THR 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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497C ASP* 2.8 33.8 + - - -
528C LEU* 1.3 68.2 - - - +
530C MET* 1.3 54.5 + - - +
531C GLY 2.8 14.3 + - - +
532C TYR* 2.9 47.4 + - + +
533C TRP* 3.6 11.2 + - - -
33D TRP* 2.8 28.7 + - + +
76D ASN* 3.4 28.7 - - + +
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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