Contacts of the strand formed by residues 471 - 478 (chain A) in PDB entry 5HLB
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 471 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A ILE* 3.9 3.2 - - - +
462A LYS* 5.8 0.7 + - - -
470A LEU* 1.3 77.8 - - - +
472A THR* 1.3 61.6 + - - +
490A GLY* 3.3 10.2 - - - -
491A SER* 2.7 47.7 + - - -
492A GLU* 4.7 1.6 + - - +
500A ARG* 3.4 40.1 + - - +
722A TRP* 4.1 3.6 - - + -
723A VAL* 3.6 8.5 - - - +
724A GLY 3.0 36.9 + - - +
725A ARG* 4.7 0.6 - - - +
726A ASP* 3.7 15.9 - - - +
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Residues in contact with THR 472 (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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454A ALA* 3.8 26.5 - - + -
458A ILE* 3.6 30.1 - - + -
471A GLU* 1.3 77.3 + - - +
473A ALA* 1.3 72.4 + - - +
474A ILE* 4.4 2.3 - - + +
488A VAL* 4.9 2.2 - - + -
490A GLY* 3.3 24.4 + - - -
491A SER 4.1 9.0 - - - +
500A ARG* 3.8 6.4 - - - -
721A THR* 4.5 0.7 - - - +
722A TRP* 3.0 21.4 + - - -
723A VAL* 3.5 9.2 - - - +
742A ILE* 4.2 14.1 - - + +
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Residues in contact with ALA 473 (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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472A THR* 1.3 80.6 + - - +
474A ILE* 1.3 62.7 + - - +
488A VAL* 3.3 14.6 - - - +
500A ARG* 4.0 16.6 - - + -
501A ALA* 4.1 1.8 - - - +
618A PRO* 3.8 21.8 - - + +
720A ILE 3.6 2.0 - - - +
721A THR* 3.5 3.1 - - - -
722A TRP* 2.9 46.6 + - + +
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Residues in contact with ILE 474 (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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450A ALA* 3.4 39.9 - - + +
453A ALA* 4.6 2.2 - - + -
454A ALA* 4.4 7.4 - - + +
472A THR* 4.4 3.6 - - - +
473A ALA* 1.3 77.1 - - - +
475A VAL* 1.3 68.0 + - - +
476A VAL* 4.3 11.2 - - + -
486A ALA 4.6 0.9 - - - -
487A MET* 3.4 4.7 - - - -
488A VAL* 2.8 49.3 + - + +
719A THR* 3.9 25.4 - - + -
720A ILE 3.4 4.9 - - - +
721A THR* 4.0 17.9 - - + +
742A ILE* 3.8 22.4 - - + -
746A TYR* 5.1 7.6 - - + -
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Residues in contact with VAL 475 (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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474A ILE* 1.3 78.6 - - - +
476A VAL* 1.3 62.8 + - - +
477A VAL* 4.0 12.6 - - + -
484A VAL* 4.8 2.9 - - + -
486A ALA 3.5 7.4 - - - +
487A MET* 4.4 10.1 - - + -
501A ALA* 3.8 23.6 - - + +
618A PRO* 3.8 21.3 - - + +
619A ILE* 3.9 19.3 - - + +
622A ALA* 3.8 27.2 - - + +
718A VAL 3.7 1.0 - - - +
719A THR* 3.4 4.5 - - - +
720A ILE* 2.9 34.6 + - + +
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Residues in contact with VAL 476 (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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446A ALA* 4.6 3.6 - - + -
450A ALA* 5.3 0.2 - - + -
474A ILE* 4.3 7.2 - - + -
475A VAL* 1.3 75.4 - - - +
477A VAL* 1.4 66.4 + - - +
484A VAL* 3.7 1.4 - - - +
485A ARG* 2.9 33.9 + - + -
486A ALA* 2.9 31.4 + - + +
717A THR* 3.8 25.4 - - + -
718A VAL 3.4 2.9 - - - -
719A THR* 3.6 22.2 - - + +
746A TYR* 3.4 37.5 - - + +
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Residues in contact with VAL 477 (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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475A VAL* 4.0 17.5 - - + -
476A VAL* 1.4 78.2 - - - +
478A ASP* 1.3 73.1 + - - +
479A ARG 3.3 0.3 + - - -
482A GLY 3.9 6.7 - - - +
483A GLU 3.4 8.3 - - - +
484A VAL* 3.8 23.6 - - + -
485A ARG* 4.2 5.4 - - - -
622A ALA* 4.0 18.8 - - + +
626A GLN* 4.2 3.8 - - + -
637A LEU* 4.1 22.0 - - + -
717A THR* 3.4 6.3 - - - -
718A VAL* 3.0 47.4 + - + +
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Residues in contact with ASP 478 (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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477A VAL* 1.3 71.9 - - - +
479A ARG* 1.3 67.9 + - - +
480A PHE* 3.0 17.5 + - - +
481A SER* 2.8 43.6 + - - +
482A GLY* 3.2 17.2 + - - -
483A GLU* 2.8 24.2 + - + +
485A ARG* 3.4 25.1 + - - +
626A GLN* 3.7 5.7 - - - +
716A SER 3.9 9.1 - - - +
717A THR* 4.8 1.1 - - - +
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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