Contacts of the strand formed by residues 454 - 462 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422C PRO* 4.2 4.5 - - - -
452C ASP 3.7 0.4 + - - -
453C ASN* 1.3 88.2 - - - +
455C THR* 1.3 63.9 + - - -
456C TYR* 3.5 9.1 - - - -
472C HIS* 4.8 1.3 - - - -
473C LEU 3.0 31.0 + - - -
487C NAG 3.7 17.5 - - - -
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Residues in contact with THR 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C SER 3.7 1.7 - - - +
422C PRO* 3.0 29.1 - - - +
454C GLY* 1.3 71.9 - - - -
456C TYR* 1.3 75.2 + - - +
457C LEU* 5.5 4.5 - - + -
470C PRO* 4.2 17.9 - - + -
471C ALA 3.4 6.7 - - - +
472C HIS* 3.4 19.5 + - + -
487C NAG 5.2 4.3 - - - -
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Residues in contact with TYR 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C PHE* 4.1 12.8 - + + -
419C TRP* 3.7 17.5 - - + -
420C LEU 3.3 15.9 - - - +
421C SER* 4.0 6.7 - - - -
422C PRO* 3.4 22.7 - - + +
427C VAL* 5.7 1.3 - - + -
435C LEU* 4.0 22.9 - - + +
443C LEU* 3.5 28.7 - - + -
445C VAL* 5.0 1.8 - - + -
452C ASP* 2.8 42.7 + - - +
454C GLY 3.5 15.5 - - - -
455C THR* 1.3 80.9 - - - +
457C LEU* 1.3 59.6 + - - +
470C PRO* 3.3 5.2 - - - +
471C ALA* 2.7 41.4 + - + +
473C LEU* 3.9 15.4 - - + +
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Residues in contact with LEU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL* 4.0 19.7 - - + -
118B ILE* 3.8 28.3 - - + -
141B VAL* 4.3 12.6 - - + -
419C TRP* 3.1 8.9 - - - -
420C LEU* 2.6 51.4 + - + +
421C SER 5.2 0.2 + - - -
455C THR* 4.4 4.0 + - + -
456C TYR* 1.3 74.1 - - - +
458C CYS* 1.3 60.3 + - - +
459C ILE* 4.1 4.6 + - + +
468C SER* 4.1 8.5 - - - -
469C MET* 3.3 30.5 - - - +
470C PRO* 3.6 14.4 - - + -
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Residues in contact with CYS 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C ILE* 3.6 16.6 - - - -
407C CYS* 2.1 47.3 - - - -
417C ILE* 4.7 0.2 - - + -
418C LEU 3.2 4.5 - - - +
419C TRP* 3.2 33.7 - - + +
457C LEU* 1.3 74.0 - - - +
459C ILE* 1.3 58.8 + - - +
468C SER* 3.2 6.1 - - - -
469C MET* 3.0 42.1 + - - -
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Residues in contact with ILE 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ILE* 3.4 33.0 - - + -
120B LEU* 4.2 26.2 - - + -
142B TYR* 5.3 1.6 - - + -
387C ILE* 4.6 0.7 - - - -
416C ALA 3.4 3.8 - - - +
417C ILE* 3.5 2.3 - - - -
418C LEU* 2.6 58.8 + - + +
420C LEU* 3.1 42.0 - - + +
426C LEU* 4.9 1.8 - - + -
457C LEU* 4.3 6.3 - - + +
458C CYS* 1.3 79.6 - - - +
460C ALA* 1.3 63.2 + - - +
461C ALA* 3.8 0.6 + - + -
466C ASN* 4.8 2.5 - - + +
467C ASP 3.2 13.7 - - - +
468C SER* 4.4 1.6 - - - -
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Residues in contact with ALA 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C ALA* 3.5 12.5 - - + +
387C ILE* 3.4 19.6 - - + +
409C ALA* 3.4 32.5 - - + -
415C PRO* 4.3 0.9 - - + -
416C ALA 3.4 4.5 - - - -
417C ILE* 3.7 7.2 - - + -
459C ILE* 1.3 72.2 - - - +
461C ALA* 1.3 59.3 + - - +
466C ASN* 3.1 6.1 - - - +
467C ASP* 2.8 35.5 + - + +
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Residues in contact with ALA 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU* 3.5 31.2 - - + -
385C ALA* 3.9 1.5 - - - +
415C PRO* 3.3 4.4 - - - +
416C ALA* 2.8 46.8 + - + +
418C LEU* 5.1 7.6 - - + -
459C ILE* 4.9 2.9 - - + +
460C ALA* 1.3 75.8 - - - +
462C ASN* 1.3 61.5 + - - +
465C GLY 3.8 4.0 - - - +
466C ASN* 3.9 1.1 - - + -
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Residues in contact with ASN 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C CYS* 5.1 0.2 - - - +
383C ARG 2.9 24.8 + - - -
384C ARG* 3.8 1.9 - - - -
385C ALA* 3.3 15.8 + - - +
411C GLY* 3.9 3.0 - - - -
412C ASP 3.7 8.9 + - - +
413C PRO* 2.8 34.5 + - + +
414C PRO 4.8 1.1 - - - +
415C PRO* 4.1 5.3 - - + +
461C ALA* 1.3 77.4 - - - +
463C ALA* 1.3 68.2 + - - +
464C GLY 2.9 11.8 + - - -
465C GLY* 2.9 32.8 + - - +
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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