Contacts of the strand formed by residues 501 - 505 (chain X) in PDB entry 2W6C
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 LYS 501 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420X LEU* 4.2 1.7 + - - +
493X PRO* 4.1 26.3 - - + +
494X LEU 4.3 11.1 - - - +
495X PHE* 3.5 30.7 + - - +
496X THR* 5.5 0.2 - - - +
499X GLU* 3.7 37.7 - - + +
500X GLN* 1.3 72.5 - - - +
502X PHE* 1.3 63.0 + - - +
512X VAL* 4.0 22.0 - - + -
513X HIS 3.2 10.1 - - - +
514X GLN* 4.1 9.6 - - + +
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Residues in contact with PHE 502 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420X LEU* 3.0 32.8 - - + +
421X TYR 4.7 0.2 - - - -
422X PHE* 3.7 28.0 - + + -
492X TRP* 5.0 3.8 - - - +
493X PRO* 5.4 2.0 - - - -
500X GLN 4.0 6.5 - - - -
501X LYS* 1.3 78.5 - - - +
503X ILE* 1.3 75.5 + - - +
504X ASP* 4.7 0.2 - - - -
512X VAL* 3.2 7.8 - - - +
513X HIS* 2.7 73.4 + + + -
514X GLN 3.7 8.1 - - - -
516X LEU* 3.5 48.7 - - + -
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Residues in contact with ILE 503 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420X LEU 3.2 3.5 + - - +
421X TYR* 4.3 2.7 - - + -
422X PHE 2.8 31.7 + - - -
492X TRP* 3.3 63.5 - - + -
493X PRO* 4.0 15.0 - - + -
502X PHE* 1.3 89.1 - - - +
504X ASP* 1.3 56.2 + - - +
505X LEU* 3.6 15.9 - - + -
510X MET* 3.5 35.7 - - + -
511X LYS 3.5 11.9 - - - +
512X VAL* 4.1 3.8 - - + -
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Residues in contact with ASP 504 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422X PHE* 3.2 19.6 - - - +
424X ASN* 4.0 7.5 + - - +
468X ARG* 4.3 1.7 + - - -
502X PHE* 4.7 0.2 - - - -
503X ILE* 1.3 81.8 - - - +
505X LEU* 1.3 76.0 + - - +
506X ASN* 3.5 26.4 + - - +
509X PRO 5.3 1.0 - - - +
510X MET* 4.1 11.8 - - - +
511X LYS* 3.4 26.5 + - - +
513X HIS* 2.6 40.1 + - - -
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Residues in contact with LEU 505 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421X TYR* 3.3 44.2 - - + -
422X PHE 3.0 6.1 + - - -
423X PHE* 3.8 23.7 - - + -
424X ASN 3.2 17.7 + - - -
425X HIS 3.8 1.7 + - - -
465X LEU* 4.2 4.5 - - - -
468X ARG* 4.1 10.1 - - - +
469X ILE* 3.9 22.7 - - + -
472X TYR* 4.0 19.3 - - + -
473X TRP* 4.3 18.4 - - + -
492X TRP* 4.8 0.7 - - + -
503X ILE* 3.6 18.8 - - + -
504X ASP* 1.3 86.2 - - - +
506X ASN* 1.3 63.1 + - - +
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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