Contacts of the strand formed by residues 445 - 452 (chain B) in PDB entry 3O8C
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 445 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B THR 3.7 0.3 - - - +
436B VAL* 3.4 5.0 - - - +
437B ASP* 2.8 40.9 + - - +
439B SER* 2.6 25.9 + - - -
441B ASP* 3.7 6.2 + - - -
444B PHE* 1.3 74.5 + - - +
446B ILE* 1.3 70.1 + - - +
447B GLU* 3.7 27.3 + - + +
601B ARG* 3.2 28.2 - - + +
603B GLY 5.7 1.3 - - - +
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Residues in contact with ILE 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B GLN* 4.2 21.8 - - + +
435B THR 3.5 4.9 - - - +
436B VAL* 3.9 24.2 - - + -
444B PHE* 4.1 15.0 - - + -
445B THR* 1.3 80.6 - - - +
447B GLU* 1.3 62.4 + - - +
448B THR* 4.3 1.1 + - - +
489B SER* 4.1 11.4 - - - -
492B CYS* 4.8 2.9 - - - -
532B TRP* 4.5 6.1 - - + -
557B PHE* 3.6 35.4 - - + -
601B ARG 2.8 14.3 + - - +
602B LEU* 3.8 39.1 - - + +
603B GLY* 4.5 1.0 + - - -
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Residues in contact with GLU 447 (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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433B THR 3.7 0.3 - - - +
434B GLN* 3.2 5.9 - - - +
435B THR* 2.9 47.8 + - - +
436B VAL 5.7 0.2 - - - -
437B ASP* 3.4 33.8 - - - +
445B THR* 3.7 21.0 - - + +
446B ILE* 1.3 73.2 - - - +
448B THR* 1.3 62.3 + - - +
449B THR* 4.6 12.3 - - + +
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Residues in contact with THR 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 3.4 30.3 - - + -
433B THR 3.5 5.8 - - - +
434B GLN* 3.9 18.2 + - + +
446B ILE* 4.3 1.8 + - - +
447B GLU* 1.3 73.9 + - - +
449B THR* 1.3 70.2 + - - +
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Residues in contact with THR 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 3.4 3.3 - - - +
433B THR* 2.8 41.6 + - - +
435B THR* 4.8 10.8 + - - +
447B GLU* 4.6 16.2 - - + +
448B THR* 1.3 86.6 - - - +
450B THR* 1.3 61.4 + - - +
451B VAL* 3.5 18.5 - - - +
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Residues in contact with THR 450 (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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350B TYR* 6.3 0.2 - - + -
369B HIS* 3.5 36.2 + - + +
430B THR* 3.9 23.6 - - + +
431B CYS 3.4 9.2 - - - +
432B VAL* 3.7 7.9 - - - +
449B THR* 1.3 73.3 - - - +
451B VAL* 1.3 67.6 + - - +
452B PRO* 4.8 0.2 - - - +
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Residues in contact with VAL 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B THR* 3.3 8.0 - - - -
431B CYS* 2.7 48.0 + - + +
433B THR* 3.7 24.7 - - + -
449B THR* 3.5 21.1 - - - +
450B THR* 1.3 80.3 - - - +
452B PRO* 1.3 81.9 - - + +
481B ARG* 3.4 19.1 - - - +
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Residues in contact with PRO 452 (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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429B ASN 3.7 8.7 - - - +
430B THR* 4.3 5.8 - - + -
450B THR 4.8 0.2 - - - +
451B VAL* 1.3 100.6 - - + +
453B GLN* 1.3 68.4 + - - +
454B ASP 3.8 0.2 + - - -
477B THR* 6.2 0.2 - - - +
480B GLU* 6.3 0.4 - - - -
481B ARG* 3.4 43.9 + - + +
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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