Contacts of the strand formed by residues 446 - 451 (chain A) in PDB entry 1HHS
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 ILE 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A LEU* 3.9 26.9 - - + -
414A GLN* 3.8 24.0 - - + +
415A LEU* 4.3 7.4 - - + -
418A THR* 4.1 5.4 - - - +
419A ALA* 4.4 3.4 - - + -
422A LEU* 3.6 29.8 - - + -
435A PHE* 4.7 0.9 - - + -
439A TYR* 3.3 22.4 - - + +
444A GLU* 3.4 10.6 + - + +
445A GLU* 1.3 77.8 - - + +
447A ARG* 1.3 68.8 + - - +
458A GLY 3.4 2.2 - - - -
459A TRP* 3.6 33.0 - - + +
464A ALA* 3.9 15.7 - - + -
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A TYR* 3.4 27.1 + - + +
316A GLU* 3.6 24.4 + - - +
317A TRP* 3.6 29.0 - - + +
414A GLN* 3.0 12.3 + - - -
439A TYR* 4.0 10.3 - - - -
442A GLY* 3.2 30.5 + - - +
443A HIS* 4.8 3.2 - - - +
444A GLU 2.9 18.5 + - - +
445A GLU* 4.6 1.5 - - - +
446A ILE* 1.3 82.7 - - - +
448A GLN* 1.3 64.9 + - - +
457A LEU* 3.7 0.2 - - - -
458A GLY 2.8 29.5 + - - +
460A THR* 3.6 25.9 - - - +
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Residues in contact with GLN 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A TYR* 3.9 5.6 - - - -
301A THR* 3.5 29.1 + - + +
317A TRP* 4.2 3.6 - - - -
407A SER* 2.7 50.8 + - - +
410A TYR* 3.7 12.4 - - - +
439A TYR* 2.9 32.1 + - + +
447A ARG* 1.3 81.3 - - - +
449A ILE* 1.3 70.5 + - - +
450A SER* 2.8 28.3 + - - -
456A MET 3.3 7.4 - - - -
457A LEU* 3.7 16.2 - - + -
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Residues in contact with ILE 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A TYR* 3.6 20.9 - - + +
301A THR 3.5 3.8 - - - -
304A HIS* 3.6 11.7 - - + +
310A LYS* 4.8 9.2 - - + +
313A LYS* 3.9 17.9 - - + -
314A VAL* 3.8 25.8 - - + -
317A TRP* 4.1 12.3 - - + -
448A GLN* 1.3 80.3 - - - +
450A SER* 1.3 64.6 + - - +
455A ALA* 3.2 2.9 - - - +
456A MET* 2.9 51.3 + - + +
496A PHE* 3.5 29.2 - - + -
514A PHE* 4.7 3.6 - - + -
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Residues in contact with SER 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A THR 3.0 10.4 + - - +
302A PHE* 3.8 24.9 - - - +
304A HIS* 3.1 16.8 + - - -
403A THR* 4.9 1.9 + - - +
406A MET* 5.9 0.2 - - - -
407A SER* 4.3 3.3 + - - -
410A TYR* 4.1 7.2 - - - -
448A GLN* 2.8 29.0 + - - -
449A ILE* 1.3 76.8 - - - +
451A LYS* 1.3 66.2 + - - +
452A SER 5.0 0.9 - - - -
454A ASP 3.4 5.2 - - - -
455A ALA* 3.6 16.6 - - - -
496A PHE* 3.7 6.7 - - - -
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Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A TYR* 3.9 24.4 + - + +
302A PHE 5.3 3.4 - - - +
304A HIS* 4.6 4.7 - - + -
399A ASP* 5.3 12.8 - - - -
403A THR* 4.2 9.0 - - - +
450A SER* 1.3 77.3 - - - +
452A SER* 1.3 77.7 + - - +
453A ASP* 3.0 1.0 + - - +
454A ASP* 2.9 24.2 + - - +
496A PHE* 4.0 0.2 - - - -
497A LEU* 3.9 34.4 - - + +
629A GLN 5.5 0.2 - - - -
630A TYR* 3.7 32.0 + - - +
631A LYS 3.7 17.6 + - - +
632A TRP 4.2 9.9 + - - -
633A THR* 5.7 1.0 - - - -
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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