Contacts of the strand formed by residues 447 - 458 (chain A) in PDB entry 2HD5
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 VAL 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A ASP* 3.0 37.0 - - - +
431A LEU 3.3 4.5 - - - +
432A ASP* 3.7 23.6 - - - +
443A HIS* 4.1 9.1 - - + -
446A ALA* 1.3 83.0 - - - +
448A TYR* 1.3 58.0 + - - +
449A ASN* 5.2 0.7 - - - +
520A LEU* 3.6 7.4 - - - +
521A ALA* 2.7 46.0 + - + +
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Residues in contact with TYR 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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398A PHE* 3.3 28.3 - + - +
399A PRO* 2.7 35.3 + - - +
402A LEU* 3.5 21.8 - - + -
430A ASP 3.2 6.1 + - - -
431A LEU* 2.9 39.0 + - + +
433A LEU* 3.8 30.1 - - + -
446A ALA 4.1 8.7 - - - -
447A VAL* 1.3 75.9 - - - +
449A ASN* 1.3 62.9 + - - +
518A TYR* 3.7 30.7 - - + -
519A GLU 3.3 7.0 - - - -
520A LEU* 3.4 40.9 - - + +
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Residues in contact with ASN 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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429A LEU 3.7 8.5 - - - +
430A ARG* 3.0 45.3 + - - +
447A VAL* 5.2 0.7 - - - +
448A TYR* 1.3 73.2 - - - +
450A LEU* 1.3 68.1 + - - +
470A ARG* 5.1 4.9 - - - +
518A TYR* 3.4 5.6 - - - -
519A GLU* 2.8 46.5 + - + +
521A ALA* 3.9 22.1 - - - +
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Residues in contact with LEU 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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427A PHE* 3.6 28.5 - - + -
428A PRO 3.9 2.9 - - - +
429A LEU* 2.9 30.2 + - + +
449A ASN* 1.3 76.2 - - - +
451A TYR* 1.3 62.5 + - - +
452A ALA 3.6 12.6 - - - +
453A VAL* 3.7 9.6 - - + -
470A ARG* 4.1 13.0 + - - -
477A TRP* 3.7 29.9 - - + -
493A VAL* 3.8 6.7 - - + -
516A LEU* 4.2 6.5 - - + -
517A PHE 3.4 19.3 - - - +
518A TYR* 3.3 36.8 - - + +
519A GLU* 4.9 1.1 - - - +
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Residues in contact with TYR 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A CYS 3.7 9.2 - - - -
234A ASN* 3.3 24.0 - - + +
235A THR* 2.7 41.3 + - + +
236A ARG 5.5 0.7 - - - -
324A PHE* 5.0 0.3 - - - -
401A ILE* 3.3 23.5 - - + +
450A LEU* 1.3 74.7 - - - +
452A ALA* 1.3 69.1 + - + +
469A CYS* 4.2 0.2 - - - +
470A ARG* 2.7 43.0 + - + +
477A TRP* 3.5 10.8 - - - -
517A PHE* 2.9 46.5 + - + -
518A TYR 3.8 11.7 - - - -
519A GLU* 3.8 36.6 - - + +
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Residues in contact with ALA 452 (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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231A CYS* 3.8 27.1 - - + +
450A LEU* 3.6 1.9 - - - +
451A TYR* 1.3 95.6 - - + +
453A VAL* 1.3 69.6 + - - +
468A TYR 3.3 10.3 - - - +
469A CYS* 4.2 5.6 - - + -
477A TRP* 3.9 2.7 - - - -
517A PHE* 2.9 38.4 + - + +
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Residues in contact with VAL 453 (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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231A CYS* 3.8 4.2 - - - -
427A PHE* 4.0 10.1 - - + -
450A LEU* 3.7 24.5 - - + -
452A ALA* 1.3 79.8 - - - +
454A SER* 1.3 65.3 + - - +
455A ASN* 3.3 24.6 + - - +
467A ALA* 3.3 5.9 - - - +
468A TYR* 2.8 42.3 + - + +
477A TRP* 4.9 0.2 - - + -
493A VAL* 3.8 16.4 - - + +
513A ALA* 3.7 20.6 - - + -
515A LEU 3.2 11.4 - - - +
516A LEU* 4.1 5.2 - - + -
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Residues in contact with SER 454 (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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227A SER* 2.7 26.9 + - - -
228A ILE* 4.3 7.9 - - - +
231A CYS* 4.1 6.8 - - - -
296A ALA* 3.9 6.9 - - - +
453A VAL* 1.3 71.9 - - - +
455A ASN* 1.3 59.9 + - - +
465A TYR* 3.6 18.4 - - - -
466A THR 3.7 0.2 - - - -
514A TYR* 3.0 27.4 + - - +
515A LEU* 2.8 34.3 + - - +
517A PHE* 4.5 0.6 - - - -
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Residues in contact with ASN 455 (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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453A VAL* 3.3 19.2 + - - +
454A SER* 1.3 73.7 - - - +
456A HIS* 1.3 59.5 + - - +
464A HIS 3.8 0.3 - - - +
465A TYR* 3.0 31.2 - - - -
466A THR* 2.9 33.5 + - - +
468A TYR* 3.2 53.2 - - - +
493A VAL 5.0 0.3 - - - +
495A THR* 3.9 2.8 + - - -
512A ASP* 3.3 19.0 - - + +
513A ALA* 3.5 13.3 + - - +
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Residues in contact with HIS 456 (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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420A LYS* 2.9 40.5 + - + +
454A SER 4.2 1.0 + - - -
455A ASN* 1.3 75.5 - - - +
457A SER* 1.3 66.8 + - - +
458A GLY* 3.7 18.6 - - - -
459A THR 3.2 25.1 - - - -
462A GLY 4.0 1.0 + - - -
463A GLY* 4.0 0.8 - - - -
464A HIS 3.5 7.4 - - - -
465A TYR* 3.6 38.6 - + + -
512A ASP* 2.9 27.6 + - - +
514A TYR* 4.3 5.3 - - + +
73B LEU* 3.7 26.1 + - + +
74B ARG 2.9 23.1 + - - -
75B GLY* 4.3 1.3 - - - -
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Residues in contact with SER 457 (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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420A LYS* 3.9 1.3 - - - +
456A HIS* 1.3 79.1 - - - +
458A GLY* 1.3 59.6 + - - +
463A GLY* 3.0 4.9 - - - -
464A HIS* 2.9 41.4 + - - -
512A ASP* 3.7 20.6 + - - -
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Residues in contact with GLY 458 (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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420A LYS* 3.2 19.9 + - - +
422A THR* 4.9 5.2 - - - +
456A HIS* 3.7 5.7 + - - -
457A SER* 1.3 77.5 + - - +
459A THR* 1.3 67.3 + - - +
462A GLY 3.6 7.6 - - - -
463A GLY* 4.2 2.0 - - - -
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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