Contacts of the strand formed by residues 388 - 394 (chain C) in PDB entry 2O2C
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 THR 388 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B VAL* 4.8 1.6 - - + -
388B THR* 3.5 31.9 - - + -
431B ILE* 3.9 22.0 - - + +
381C ILE* 6.0 0.2 - - - +
386C ALA* 3.4 4.6 - - - +
387C VAL* 1.3 84.8 - - + +
389C HIS* 1.3 62.7 + - - +
430C PRO* 4.4 2.3 - - - +
431C ILE* 3.3 10.8 - - + -
433C PHE* 4.1 11.2 - - - -
453C ASN* 5.6 0.2 - - - +
454C LEU 4.2 3.0 + - - -
455C ILE* 3.4 29.8 - - - +
456C PRO* 3.3 22.8 - - - +
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Residues in contact with HIS 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C GLY* 6.0 5.6 - - - -
381C ILE* 6.4 0.2 - - + -
388C THR* 1.3 76.3 - - - +
390C ALA* 1.3 61.4 + - - +
391C ILE* 3.8 19.2 + - + +
430C PRO* 4.3 12.3 - - + -
431C ILE 2.9 5.6 + - - +
432C ILE* 3.4 28.6 - - + +
433C PHE* 3.2 25.6 + - - +
455C ILE* 4.6 0.4 - - - -
456C PRO* 3.5 33.4 + - + +
458C ASP* 3.0 40.7 + - - -
527C ASN* 4.9 6.1 - - - -
549C LYS* 3.6 21.8 + - - -
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Residues in contact with ALA 390 (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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389C HIS* 1.3 75.0 - - - +
391C ILE* 1.3 62.2 + - - +
392C LEU* 3.8 16.4 - - + -
433C PHE* 3.2 29.4 - - + +
448C ILE* 4.6 1.8 - - + -
455C ILE* 4.1 2.3 - - + +
456C PRO 2.9 8.4 + - - +
457C CYS* 3.5 25.2 - - - -
458C ASP* 2.8 29.9 + - - +
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Residues in contact with ILE 391 (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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389C HIS* 3.8 15.7 - - + +
390C ALA* 1.3 71.4 - - - +
392C LEU* 1.3 60.3 + - - +
393C PRO* 3.4 18.5 - - + +
401C LEU* 4.5 3.8 - - + -
402C PRO* 3.6 19.5 - - + +
405C LEU* 3.8 30.7 - - + -
432C ILE* 3.8 25.6 - - + -
433C PHE 2.9 9.0 + - - +
434C GLY* 3.5 19.9 - - - -
458C ASP* 3.8 13.0 - - + +
460C ILE* 4.4 13.5 - - + -
546C TYR* 3.6 25.8 - - + +
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Residues in contact with LEU 392 (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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390C ALA* 4.1 10.3 - - + -
391C ILE* 1.3 82.4 - - - +
393C PRO* 1.4 62.9 - - - +
394C TYR* 3.5 13.9 - - + -
434C GLY* 4.2 4.9 - - - -
435C GLU 3.8 15.3 - - - +
437C GLY 4.9 0.4 - - - +
444C PHE* 3.8 28.9 - - + -
445C TYR* 3.2 35.4 - - + +
448C ILE* 4.5 2.2 - - + -
457C CYS* 3.8 20.2 - - + -
458C ASP 2.8 15.3 + - - +
459C PHE* 3.5 26.8 - - + -
460C ILE* 3.2 18.3 + - - -
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Residues in contact with PRO 393 (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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391C ILE* 3.4 15.7 - - + +
392C LEU* 1.4 82.6 - - - +
394C TYR* 1.3 61.5 + - - +
395C ASP 3.1 5.9 + - - -
398C LEU* 3.5 51.6 - - + +
401C LEU* 4.3 9.9 - - + -
402C PRO* 3.9 13.9 - - + -
435C GLU 3.8 8.3 - - - +
436C ALA* 3.2 11.9 - - - +
437C GLY 3.0 17.2 + - - -
460C ILE* 3.5 11.0 - - + +
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Residues in contact with TYR 394 (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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392C LEU* 3.5 13.5 - - + -
393C PRO* 1.3 69.4 - - - +
395C ASP* 1.3 62.6 + - - +
437C GLY* 3.8 16.8 - - - -
438C THR* 3.9 8.3 - - + -
441C GLN* 2.7 29.5 + - - +
445C TYR* 3.0 33.4 + - - -
459C PHE* 3.5 25.6 - + - -
460C ILE 2.6 17.7 + - - +
461C GLY* 4.0 9.1 - - - -
462C ALA* 4.5 3.3 + - - +
473C HIS* 5.9 0.2 + - - -
476C PHE* 3.2 44.2 - + + -
477C MET* 4.8 3.0 - - - +
480C PHE* 3.6 46.4 - + + -
483C GLN* 3.7 2.1 - - - +
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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