Contacts of the strand formed by residues 530 - 535 (chain C) in PDB entry 5HP1
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 LYS 530 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428C GLN 5.6 1.1 - - - -
430C GLU* 3.7 29.6 + - - +
434C ILE* 3.5 27.4 - - + +
491C LEU 3.1 4.1 + - - +
492C GLU* 3.2 32.7 + - + +
493C VAL* 3.1 23.4 + - - +
528C LYS 3.8 0.4 - - - -
529C GLU* 1.3 87.9 - - + +
531C VAL* 1.3 65.3 + - - +
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Residues in contact with VAL 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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428C GLN 4.8 4.5 + - - +
429C LEU* 3.4 19.5 - - + +
430C GLU* 2.6 37.7 + - - +
486C LEU* 4.4 5.4 - - + -
493C VAL* 3.5 17.9 - - + +
495C ILE* 4.7 4.9 - - + -
525C LEU* 4.0 29.4 - - + +
528C LYS* 3.5 32.3 - - + -
530C LYS* 1.3 79.5 - - - +
532C TYR* 1.3 63.1 + - - +
533C LEU* 4.6 8.7 - - + -
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Residues in contact with TYR 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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430C GLU* 3.4 27.4 - - + +
431C LYS 3.5 21.6 + - - -
432C GLU 3.5 15.7 - - - +
433C PRO* 3.5 19.7 - - + +
434C ILE* 4.0 2.4 - - + +
493C VAL 3.1 7.7 + - - +
494C ASN* 3.4 14.6 - - - +
495C ILE* 2.9 30.0 + - - +
531C VAL* 1.3 74.2 - - - +
533C LEU* 1.3 74.2 + - - +
534C ALA* 3.6 10.2 - - + +
255D ASN* 2.7 34.2 + - - -
259D LYS* 3.5 19.9 - - - -
289D LEU* 3.5 22.7 - - + -
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Residues in contact with LEU 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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429C LEU* 3.9 26.1 - - + +
430C GLU 5.1 1.5 + - - +
482C ILE* 4.8 11.2 - - + -
495C ILE* 3.5 35.4 - - + +
497C THR* 4.7 5.4 - - + -
503C LEU* 3.7 33.8 - - + +
506C ILE* 3.5 35.4 - - + -
507C GLN* 5.1 8.2 + - + +
525C LEU* 5.8 1.1 - - + -
531C VAL* 4.1 10.4 + - + +
532C TYR* 1.3 87.6 - - - +
534C ALA* 1.3 60.8 + - - +
259D LYS* 5.0 1.7 + - - -
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Residues in contact with ALA 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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495C ILE 3.0 10.5 + - - +
496C VAL* 3.4 16.6 - - + +
497C THR* 3.0 27.7 + - - +
503C LEU* 4.3 4.7 - - - -
532C TYR* 3.6 28.5 - - + +
533C LEU* 1.3 75.9 - - - +
535C TRP* 1.3 62.0 + - - +
255D ASN* 4.4 4.5 - - - +
258D GLN* 4.8 6.5 - - + +
259D LYS* 4.2 9.4 - - - +
289D LEU* 4.5 1.1 - - + -
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Residues in contact with TRP 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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497C THR 3.4 4.9 - - - -
498C ASP 3.5 31.8 + - - -
499C SER 4.2 4.7 - - - -
500C GLN* 3.6 35.3 - - + +
503C LEU* 3.5 20.4 - - + +
534C ALA* 1.3 74.9 - - - +
536C VAL* 1.3 74.3 + - - +
537C PRO* 3.6 39.3 - - + -
538C ALA 5.1 0.4 - - - -
258D GLN* 4.9 5.5 - - - +
259D LYS* 4.0 17.2 + - - +
262D GLY* 4.3 8.0 - - - -
265D ASN* 4.9 6.5 - - - -
266D TRP* 5.7 7.0 - + - -
422D LEU* 4.0 33.9 - - + +
423D VAL* 3.9 28.5 - - + -
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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