Contacts of the strand formed by residues 454 - 462 (chain B) 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 454 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422B PRO* 3.7 7.6 - - - -
452B ASP 3.8 0.4 + - - -
453B ASN* 1.3 76.4 - - - +
455B THR* 1.3 64.4 + - - -
456B TYR* 3.6 6.9 - - - -
473B LEU 2.9 32.8 + - - -
488B NAG 3.6 23.1 - - - -
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Residues in contact with THR 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B LEU 4.1 1.4 - - - +
421B SER 4.3 0.2 - - - -
422B PRO* 3.3 22.8 - - - +
454B GLY* 1.3 73.7 - - - -
456B TYR* 1.3 63.3 + - - +
470B PRO* 5.8 2.7 - - - -
471B ALA 3.6 4.5 - - - -
472B HIS* 3.3 33.9 - - + +
488B NAG 4.2 6.3 - - - +
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Residues in contact with TYR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B PHE* 3.8 19.3 - + + -
419B TRP* 4.0 15.7 - + + -
420B LEU 3.4 5.6 - - - -
421B SER* 3.7 23.1 - - - -
422B PRO* 3.4 21.8 - - + +
427B VAL* 6.1 0.4 - - + -
435B LEU* 4.5 9.7 - - + +
443B LEU* 3.7 26.5 - - + -
445B VAL* 4.4 6.0 - - + +
452B ASP* 2.9 46.9 + - - +
454B GLY 3.6 9.0 - - - -
455B THR* 1.3 78.4 - - - +
457B LEU* 1.3 60.4 + - - +
458B CYS 4.2 0.7 - - - -
470B PRO* 3.3 5.9 - - - +
471B ALA* 2.5 42.9 + - + +
473B LEU* 3.7 20.4 - - + +
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Residues in contact with LEU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LYS* 5.4 9.9 - - - +
94A LEU* 6.1 2.0 - - + -
117A VAL* 4.2 29.6 - - + -
118A ILE* 5.7 0.9 - - + -
418B LEU 3.5 0.9 - - - +
419B TRP* 3.4 8.1 - - - -
420B LEU* 2.7 53.9 + - + +
456B TYR* 1.3 75.5 - - - +
458B CYS* 1.3 62.7 + - - +
459B ILE* 3.9 18.7 + - + +
468B SER* 3.2 28.5 - - - +
469B MET 3.6 17.3 - - - +
470B PRO* 3.9 13.5 - - + -
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Residues in contact with CYS 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B ILE* 3.8 3.4 - - + +
407B CYS* 2.0 50.9 - - - -
417B ILE* 3.6 19.1 - - - -
418B LEU 3.5 2.7 - - - -
419B TRP* 3.5 22.5 - - + -
457B LEU* 1.3 72.7 - - - +
459B ILE* 1.3 64.0 + - - +
460B ALA 4.2 0.2 - - - -
468B SER* 3.1 9.5 + - - -
469B MET* 2.8 43.0 + - + +
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Residues in contact with ILE 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 4.4 13.0 - - + -
118A ILE* 3.9 40.4 - - + -
120A LEU* 4.3 25.4 - - + -
416B ALA 3.6 1.7 - - - +
417B ILE* 3.4 3.1 - - - +
418B LEU* 2.7 51.0 + - + +
420B LEU* 4.9 7.0 - - + -
426B LEU* 5.0 4.9 - - + -
457B LEU* 4.4 25.8 - - + +
458B CYS* 1.3 81.5 - - - +
460B ALA* 1.3 68.5 + - - +
461B ALA* 4.9 3.1 - - + -
466B ASN* 4.9 1.3 - - + -
467B ASP 3.4 8.5 - - - +
468B SER* 4.6 5.2 - - - +
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Residues in contact with ALA 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B ALA* 3.4 10.1 - - + +
387B ILE* 4.0 14.1 - - + +
407B CYS* 5.6 0.2 - - - -
409B ALA* 3.6 31.6 - - + -
415B PRO* 4.1 5.2 - - + -
416B ALA 3.4 4.9 - - - -
417B ILE* 3.6 9.0 - - + -
458B CYS 4.2 0.2 - - - -
459B ILE* 1.3 72.3 - - - +
461B ALA* 1.3 60.9 + - - +
466B ASN* 3.2 4.9 - - - +
467B ASP* 3.0 33.9 + - + +
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Residues in contact with ALA 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 5.8 5.2 - - + -
120A LEU* 4.8 11.7 - - + -
385B ALA* 4.0 3.3 - - - +
414B PRO 4.7 0.2 - - - +
415B PRO* 3.4 3.7 - - - +
416B ALA* 3.1 37.5 + - + +
418B LEU* 6.2 4.3 - - + -
459B ILE* 4.1 4.5 - - + -
460B ALA* 1.3 75.2 - - - +
462B ASN* 1.3 62.5 + - - +
465B GLY 4.0 3.6 - - - -
466B ASN* 4.0 16.6 - - + +
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Residues in contact with ASN 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.8 16.2 - - - +
383B ARG 2.8 25.9 + - - -
385B ALA* 3.3 14.1 + - - +
411B GLY* 4.0 2.0 - - - -
412B ASP 3.4 11.9 + - - +
413B PRO* 2.9 36.0 + - + +
414B PRO 4.6 1.3 - - - +
415B PRO* 4.5 3.1 - - + -
461B ALA* 1.3 77.2 - - - +
463B ALA* 1.3 64.4 + - - +
464B GLY* 3.1 12.0 + - - +
465B GLY* 2.9 28.9 + - - +
466B ASN* 5.5 0.3 + - - +
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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