Contacts of the strand formed by residues 530 - 535 (chain D) in PDB entry 1HVU
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428D GLN 5.9 1.1 - - - -
430D GLU* 5.5 7.0 - - + -
434D ILE* 5.1 10.5 - - + -
491D LEU 2.8 9.9 + - - +
492D GLU* 3.1 16.6 - - + -
493D VAL* 2.9 25.8 + - - +
528D LYS* 3.8 3.0 - - - +
529D GLU* 1.3 76.7 - - + +
531D VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D GLN 5.0 5.6 + - - +
429D LEU* 3.5 10.9 - - + -
430D GLU* 2.6 36.0 + - - +
493D VAL* 3.6 7.4 - - + +
525D LEU* 6.1 6.1 - - + +
528D LYS* 5.3 9.0 - - + -
530D LYS* 1.3 75.7 - - - +
532D TYR* 1.3 55.9 + - - +
533D LEU* 4.1 2.0 - - + +
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Residues in contact with TYR 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D LEU* 5.2 0.4 - - - -
430D GLU* 3.9 22.9 - - + +
432D GLU 4.3 0.9 - - - +
433D PRO* 4.1 24.5 - - + -
434D ILE* 4.5 5.8 - - + +
493D VAL 3.2 9.9 + - - +
494D ASN* 3.5 6.6 - - + +
495D ILE* 2.9 27.8 + - - +
531D VAL* 1.3 75.5 - - - +
533D LEU* 1.3 60.1 + - - +
534D ALA* 3.8 2.1 + - - +
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Residues in contact with LEU 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D LEU* 5.2 9.3 - - + +
430D GLU 5.5 0.6 + - - -
495D ILE* 3.5 10.5 - - + +
503D LEU* 6.0 6.1 - - + +
506D ILE* 5.6 11.0 - - + -
531D VAL* 4.1 2.5 - - + +
532D TYR* 1.3 72.2 - - - +
534D ALA* 1.3 59.2 + - - +
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Residues in contact with ALA 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D ILE 2.9 13.9 + - - +
496D VAL* 3.4 10.1 - - + -
497D THR* 2.8 26.0 + - - -
503D LEU* 5.9 1.9 - - - +
532D TYR* 3.8 2.0 + - + +
533D LEU* 1.3 75.0 - - - +
535D TRP* 1.3 63.9 + - - +
255E ASN* 5.2 14.6 - - + -
258E GLN* 6.5 0.7 - - + -
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Residues in contact with TRP 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D VAL* 5.9 1.1 - - - -
497D THR* 3.3 9.9 - - - +
499D SER 5.5 5.4 - - - +
500D GLN* 5.9 2.0 - - - +
503D LEU* 5.0 15.7 - - + -
534D ALA* 1.3 79.3 - - - +
536D VAL* 1.3 60.7 + - - +
258E GLN* 4.9 11.9 - - - +
259E LYS* 5.7 1.9 - - - -
262E GLY* 5.6 2.6 - - - -
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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