Contacts of the strand formed by residues 383 - 387 (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 ARG 383 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378C ASN* 5.8 3.6 - - - +
381C THR* 6.0 0.9 - - - +
382C CYS* 1.3 72.0 - - - +
384C ARG* 1.3 62.6 - - - +
410C ASP* 6.2 2.0 - - - +
411C GLY* 3.3 12.9 + - - +
412C ASP* 3.0 47.0 + - + +
462C ASN* 2.9 22.6 + - - -
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Residues in contact with ARG 384 (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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94B LEU* 4.0 30.0 - - - +
96B PRO* 4.3 20.0 - - + +
382C CYS 3.6 5.8 + - - +
383C ARG* 1.3 74.6 - - - +
385C ALA* 1.3 70.9 + - - +
386C ARG* 3.3 51.2 + - - +
410C ASP 3.8 4.0 - - - +
411C GLY* 4.1 1.6 - - - -
462C ASN* 3.8 6.7 - - - -
464C GLY* 3.6 23.8 - - - +
465C GLY* 4.2 7.0 - - - +
466C ASN 5.1 2.4 + - - +
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Residues in contact with ALA 385 (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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383C ARG 3.6 0.2 + - - -
384C ARG* 1.3 75.1 + - - +
386C ARG* 1.3 64.5 + - - +
410C ASP 3.3 8.5 - - - -
415C PRO* 3.7 28.3 - - + -
460C ALA* 3.5 27.6 - - + +
461C ALA 3.9 1.6 - - - +
462C ASN* 3.3 13.4 + - - +
465C GLY 4.0 10.5 + - - +
466C ASN* 4.0 6.3 - - - +
467C ASP* 3.3 15.2 - - - +
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Residues in contact with ARG 386 (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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384C ARG* 3.3 52.7 + - + +
385C ALA* 1.3 81.8 - - - +
387C ILE* 1.3 65.9 + - - +
388C ARG* 3.4 0.9 + - - -
390C ARG* 5.4 3.8 - - - +
409C ALA* 4.1 3.8 - - - +
410C ASP* 2.9 38.5 + - + +
467C ASP* 3.4 11.7 - - - +
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Residues in contact with ILE 387 (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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386C ARG* 1.3 71.2 - - - +
388C ARG* 1.3 67.7 + - - +
389C ASP* 3.8 18.6 - - + +
390C ARG* 2.7 35.4 + - - +
407C CYS* 3.7 15.5 - - - -
408C ARG 3.6 13.2 - - - +
409C ALA* 4.3 1.6 - - + +
458C CYS* 3.6 25.6 - - - +
460C ALA* 3.4 34.3 - - + +
467C ASP* 3.0 23.8 + - - +
468C SER 4.3 3.1 - - - -
469C MET* 4.0 16.6 - - + -
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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