Contacts of the strand formed by residues 465 - 475 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C PRO* 3.6 21.3 - - - -
97C LEU 4.0 7.2 + - - +
384D ARG* 3.6 10.1 - - - -
385D ALA* 3.5 7.4 + - - +
462D ASN* 3.0 32.4 + - - +
463D ALA 3.4 2.4 + - - -
464D GLY* 1.3 79.4 - - - +
466D ASN* 1.3 60.1 + - - -
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Residues in contact with ASN 466 (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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94C LEU* 3.5 28.9 - - + +
95C ILE 3.0 21.6 + - - -
96C PRO* 3.4 18.3 - - - +
97C LEU* 4.4 5.1 - - - +
120C LEU* 3.6 24.0 - - - +
384D ARG* 3.1 27.6 + - - +
385D ALA* 4.0 4.1 - - - +
459D ILE* 4.6 2.2 - - + -
460D ALA 3.2 14.1 - - - +
461D ALA* 3.8 12.8 - - + +
465D GLY* 1.3 73.9 - - - +
467D ASP* 1.3 64.1 + - - +
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Residues in contact with ASP 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU* 3.7 6.3 - - - -
385D ALA 3.6 12.8 - - - +
386D ARG* 3.7 11.7 - - - +
387D ILE* 3.2 26.9 + - + +
390D ARG* 2.7 30.9 + - - -
459D ILE* 3.4 4.0 - - - +
460D ALA 2.8 34.0 + - - +
466D ASN* 1.3 76.2 - - - +
468D SER* 1.3 85.9 + - - +
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Residues in contact with SER 468 (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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93C LYS* 5.9 1.7 - - - +
94C LEU* 3.7 23.2 - - - +
387D ILE* 3.9 1.3 - - - -
390D ARG* 2.7 30.1 + - - -
457D LEU* 4.0 27.9 - - - +
458D CYS 3.2 9.4 - - - -
459D ILE* 4.5 2.2 - - - -
467D ASP* 1.3 78.3 + - - +
469D MET* 1.3 56.2 + - - +
470D PRO* 4.7 1.6 - - - +
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Residues in contact with MET 469 (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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387D ILE* 3.7 22.0 - - + -
389D ASP* 3.2 28.7 - - - +
390D ARG* 4.1 15.7 - - - +
391D LYS 4.5 10.5 - - - +
392D ALA* 6.0 0.7 - - - -
393D GLN* 3.4 29.6 - - - +
406D VAL 3.9 9.9 - - - +
407D CYS* 4.3 13.9 - - - -
419D TRP* 4.8 3.3 - - + -
457D LEU* 4.1 3.6 - - - +
458D CYS* 3.0 30.6 + - + +
468D SER* 1.3 76.8 - - - +
470D PRO* 1.3 81.6 - - + +
471D ALA 4.1 0.2 + - - -
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Residues in contact with PRO 470 (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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390D ARG* 5.5 1.6 - - - +
392D ALA* 4.4 10.9 - - + +
393D GLN 4.3 9.2 + - - -
455D THR* 4.1 14.8 - - + -
456D TYR 3.3 11.2 - - - +
457D LEU* 4.1 13.4 - - + -
468D SER 4.7 0.7 - - - +
469D MET* 1.3 101.5 - - + +
471D ALA* 1.3 62.1 + - - +
472D HIS* 4.5 12.3 - - + -
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Residues in contact with ALA 471 (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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393D GLN* 3.7 22.7 - - + +
405D PHE* 3.6 32.5 - - + -
419D TRP* 4.3 13.9 - - + -
455D THR* 3.4 4.7 - - - +
456D TYR* 2.8 33.1 + - + +
469D MET* 4.1 0.4 + - + -
470D PRO* 1.3 76.0 - - - +
472D HIS* 1.3 65.7 + - - +
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Residues in contact with HIS 472 (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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392D ALA* 4.9 9.8 - - + +
393D GLN 2.8 16.7 + - - +
394D GLN* 3.6 23.4 + - - +
395D VAL* 3.0 30.3 + - - +
405D PHE* 3.9 3.4 - - - -
454D GLY 3.7 2.0 - - - -
455D THR* 3.2 31.2 + - - +
470D PRO* 4.5 18.4 - - + -
471D ALA* 1.3 78.1 - - - +
473D LEU* 1.3 60.5 + - - +
474D HIS* 3.8 12.8 - + - +
485D NAG 3.5 22.2 - - - +
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Residues in contact with LEU 473 (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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395D VAL* 3.5 24.2 - - + +
397D VAL* 3.6 32.5 - - + -
403D VAL* 4.3 9.0 - - + -
405D PHE* 3.6 14.9 - - + -
445D VAL* 4.9 13.9 - - + -
448D ALA* 5.2 2.9 - - + -
452D ASP* 3.5 22.9 - - + +
453D ASN* 3.3 5.0 - - - +
454D GLY 3.1 22.3 + - - +
456D TYR* 3.5 32.3 - - + +
471D ALA 4.3 0.2 + - - -
472D HIS* 1.3 72.1 - - - +
474D HIS* 1.3 62.0 + - - +
475D VAL* 4.8 4.0 - - + -
485D NAG 3.0 13.1 + - - -
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Residues in contact with HIS 474 (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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394D GLN* 2.7 28.8 + - - -
395D VAL 2.8 19.5 + - - +
396D PHE* 3.3 45.7 - + + +
397D VAL* 2.8 29.5 + - - +
453D ASN* 3.8 3.6 - - - -
472D HIS* 3.8 8.8 - + + +
473D LEU* 1.3 75.8 - - - +
475D VAL* 1.3 59.7 + - - +
476D ARG* 4.2 2.2 + - + +
485D NAG 3.3 42.3 + - - -
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Residues in contact with VAL 475 (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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397D VAL* 3.4 19.3 - - + +
399D GLU* 4.4 12.8 - - - -
448D ALA* 5.0 2.0 - - + -
449D GLN* 4.0 13.2 - - - +
450D VAL* 4.0 33.0 - - + +
452D ASP 4.4 1.8 - - - -
453D ASN* 3.7 44.7 + - + +
473D LEU* 4.8 4.3 - - + +
474D HIS* 1.3 73.7 - - - +
476D ARG* 1.3 72.4 + - - +
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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