Contacts of the strand formed by residues 492 - 495 (chain C) in PDB entry 6T8O
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 ALA 492 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438C THR 4.4 5.6 - - - +
439C VAL* 4.7 7.4 - - + -
483C ILE* 4.3 19.3 - - + -
487C SER* 3.7 21.8 - - - +
488C THR 2.9 6.1 + - - +
489C PRO* 3.2 28.1 - - - +
491C GLU* 1.3 76.5 - - - +
493C ARG* 1.3 63.3 + - - +
494C LEU* 5.8 0.9 - - + -
512C HIS* 3.5 9.3 - - + -
588C PRO* 4.1 1.6 - - - -
589C THR* 3.6 12.1 - - - +
591C VAL* 5.9 0.4 - - + -
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Residues in contact with ARG 493 (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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489C PRO* 2.6 35.5 + - - +
490C SER* 4.7 1.6 - - - +
492C ALA* 1.3 77.6 + - - +
494C LEU* 1.3 69.1 + - - +
511C PRO 4.1 7.2 + - - -
512C HIS* 3.3 26.2 - - - -
513C LEU 3.8 7.9 - - - -
514C LEU* 3.5 36.4 - - + +
588C PRO* 4.3 16.8 - - + +
589C THR 3.0 7.9 + - - +
590C ILE* 3.4 19.9 - - + -
591C VAL 2.9 24.1 + - - -
715C ASP* 2.9 34.4 + - - +
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Residues in contact with LEU 494 (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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480C LEU* 4.1 20.9 - - + -
483C ILE* 4.4 21.1 - - + -
484C LEU* 4.8 10.8 - - + -
493C ARG* 1.3 79.1 - - - +
495C ILE* 1.3 67.9 + - - +
496C MET* 3.7 26.2 - - + -
510C ILE* 4.3 6.5 - - + -
512C HIS* 2.4 38.0 + - + +
513C LEU* 3.6 11.5 - - + -
514C LEU* 3.2 27.5 + - - +
591C VAL* 3.3 33.0 - - + +
593C VAL* 5.3 1.3 - - + -
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Residues in contact with ILE 495 (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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494C LEU* 1.3 79.2 - - - +
496C MET* 1.3 68.7 + - - +
497C ILE* 4.9 3.1 - - + -
513C LEU* 4.9 0.4 - - - -
514C LEU* 3.8 27.1 - - + -
515C CYS* 4.0 16.6 - - - -
527C ALA* 4.5 16.8 - - + +
528C LEU* 6.1 0.4 - - + -
530C TRP* 4.0 3.4 - - + -
531C SER* 3.5 23.8 - - - +
590C ILE* 4.0 8.5 - - + -
591C VAL 2.8 8.5 + - - -
592C VAL* 3.8 27.6 - - + -
593C VAL* 2.8 31.2 + - - +
720C ILE* 3.9 17.3 - - + -
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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