Contacts of the strand formed by residues 465 - 476 (chain A) in PDB entry 2ID5
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 GLY 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A ARG* 3.8 9.2 - - - -
385A ALA* 3.6 4.6 - - - +
461A ALA* 5.0 0.2 - - - -
462A ASN* 2.7 36.9 + - - +
463A ALA 3.1 1.9 - - - -
464A GLY* 1.3 79.9 - - - +
466A ASN* 1.3 62.3 + - - -
94D LEU* 4.0 14.1 - - - -
96D PRO* 5.2 2.2 - - - -
97D LEU 5.6 0.2 - - - -
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Residues in contact with ASN 466 (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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384A ARG* 5.0 0.5 + - - -
385A ALA 4.0 6.7 - - - +
460A ALA 3.1 12.6 - - - +
461A ALA* 3.9 1.8 - - + -
465A GLY* 1.3 76.2 - - - +
467A ASP* 1.3 65.6 + - - +
468A SER* 5.5 0.5 + - - -
93D LYS 5.3 2.3 - - - +
94D LEU* 3.4 42.8 - - - +
118D ILE* 3.4 32.9 + - + +
120D LEU* 3.8 31.0 - - + +
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Residues in contact with ASP 467 (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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385A ALA 3.6 14.6 - - - +
386A ARG* 3.6 14.3 - - - +
387A ILE* 2.9 24.0 + - + +
390A ARG* 2.6 42.4 + - - -
459A ILE* 3.3 6.3 - - - +
460A ALA* 2.7 31.7 + - + +
466A ASN* 1.3 79.6 - - - +
468A SER* 1.3 68.3 + - - +
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Residues in contact with SER 468 (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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387A ILE* 3.9 1.8 - - - -
390A ARG* 4.3 3.8 + - - -
457A LEU* 4.0 24.2 - - - +
458A CYS 2.9 11.7 - - - -
459A ILE* 4.4 5.6 - - - -
466A ASN* 5.5 0.5 + - - -
467A ASP* 1.3 84.9 + - - +
469A MET* 1.3 70.5 + - - +
470A PRO* 4.5 2.6 - - - +
117D VAL* 4.1 26.0 - - - +
118D ILE* 5.0 6.3 - - - +
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Residues in contact with MET 469 (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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387A ILE* 4.0 19.1 - - + -
389A ASP 3.4 24.5 - - - +
390A ARG* 3.5 44.9 - - - +
391A LYS 3.4 22.7 - - - +
392A ALA* 3.7 12.1 - - + +
393A GLN* 4.9 5.2 - - + +
407A CYS* 5.4 0.4 - - - -
457A LEU* 3.7 3.8 - - - -
458A CYS* 2.8 40.5 + - + +
468A SER* 1.3 78.4 - - - +
470A PRO* 1.3 80.1 - - + +
471A ALA* 4.9 0.5 - - - +
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Residues in contact with PRO 470 (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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392A ALA* 4.1 7.9 - - + +
393A GLN* 4.0 14.6 + - - +
455A THR* 4.0 18.2 - - + -
456A TYR 3.5 6.1 - - - +
457A LEU* 4.3 12.3 - - + -
468A SER 4.5 2.2 - - - +
469A MET* 1.3 107.4 - - + +
471A ALA* 1.3 60.7 + - - +
472A HIS* 4.1 16.2 - - + +
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Residues in contact with ALA 471 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A GLN* 3.7 16.2 - - + +
405A PHE* 3.7 28.9 - - + -
419A TRP* 3.8 26.7 - - + -
455A THR* 3.3 1.7 - - - -
456A TYR* 2.6 38.9 + - + +
470A PRO* 1.3 75.1 - - - +
472A HIS* 1.3 62.9 + - - +
473A LEU 4.1 0.3 + - - -
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Residues in contact with HIS 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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392A ALA* 4.2 14.3 - - + +
393A GLN 3.0 18.3 + - - -
394A GLN* 3.5 22.9 + - + -
395A VAL 3.3 25.8 + - - +
405A PHE* 3.6 5.6 - - - -
454A GLY 3.4 3.1 - - - -
455A THR* 2.8 38.2 + - + -
470A PRO* 4.1 16.3 - - + +
471A ALA* 1.3 73.6 - - - +
473A LEU* 1.3 61.1 + - - +
474A HIS* 3.6 19.5 - + - +
491A NAG 3.8 11.6 + - - -
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Residues in contact with LEU 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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395A VAL* 3.8 28.5 - - + +
397A VAL* 3.8 22.4 - - + -
403A VAL* 3.9 8.5 - - + -
405A PHE* 3.7 14.5 - - + -
445A VAL* 4.4 21.8 - - + -
448A ALA* 5.2 0.4 - - + -
452A ASP* 3.4 28.3 - - + +
453A ASN* 3.0 16.6 - - - +
454A GLY 2.8 24.4 + - - +
456A TYR* 4.1 12.3 - - + -
472A HIS* 1.3 71.6 - - - +
474A HIS* 1.3 60.1 + - - +
475A VAL* 3.9 17.0 - - + -
491A NAG 3.9 3.2 - - - +
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Residues in contact with HIS 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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394A GLN* 3.4 34.3 + - + +
395A VAL 3.1 16.0 + - - -
396A PHE* 3.5 40.9 - + + +
397A VAL 3.0 25.6 + - - +
453A ASN* 3.7 4.0 - - - -
472A HIS* 3.6 14.3 - + + +
473A LEU* 1.3 72.2 - - - +
475A VAL* 1.3 62.1 + - - +
476A ARG* 3.8 6.1 + - + +
491A NAG 3.5 35.6 + - - -
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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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397A VAL* 3.3 25.8 - - + +
399A GLU* 3.8 30.5 - - + +
448A ALA* 4.0 4.9 - - + -
449A GLN 3.4 31.9 - - - +
450A VAL* 4.3 14.8 - - + +
453A ASN* 3.5 20.1 + - + +
473A LEU* 3.9 20.6 - - + -
474A HIS* 1.3 72.4 - - - +
476A ARG* 1.3 62.6 + - - +
477A SER 4.1 0.7 + - - -
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Residues in contact with ARG 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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396A PHE* 3.3 43.7 - - - +
397A VAL 3.1 8.0 + - - +
398A ASP* 3.6 22.9 - - - +
399A GLU* 3.2 25.5 + - - +
474A HIS* 4.3 9.8 - - + +
475A VAL* 1.3 74.6 - - - +
477A SER* 1.3 62.0 + - - +
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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