Contacts of the strand formed by residues 520 - 523 (chain C) in PDB entry 1R4N
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 TYR 520 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C GLY 3.6 2.5 - - - +
162C MET* 2.8 56.5 + - + +
496C PHE* 3.8 31.4 - + - -
497C LEU* 5.0 4.5 - - + -
500C ALA* 4.9 0.7 - - + -
516C PHE* 4.0 9.9 - + + -
519C THR* 1.3 74.7 - - - +
521C ILE* 1.3 71.8 + - - +
522C TYR* 4.2 10.8 - - + -
529C SER* 2.8 39.1 + - - -
530C ALA* 3.6 9.6 - - - -
531C THR* 3.9 10.3 - - + +
324D PHE* 4.8 1.7 - - - -
330D LEU* 3.2 53.8 - - + +
332D THR* 4.3 5.7 - - - +
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Residues in contact with ILE 521 (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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159C VAL* 4.6 4.0 - - + -
160C GLY 3.4 5.4 - - - +
161C TYR* 4.4 8.7 - - + -
422C GLU* 3.6 31.9 - - + +
425C LEU* 4.0 17.0 - - + -
426C TYR* 3.6 36.8 - - + +
429C LEU* 6.0 0.7 - - + -
519C THR* 3.9 15.9 - - + -
520C TYR* 1.3 83.3 - - - +
522C TYR* 1.3 63.0 + - - +
523C SER 4.2 0.2 + - - -
528C THR 4.0 0.2 - - - +
529C SER* 3.0 7.5 - - - -
530C ALA 2.8 38.2 + - - +
532C PHE* 3.8 21.8 - - + -
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Residues in contact with TYR 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU 3.6 0.7 - - - +
159C VAL* 3.2 8.0 - - - +
160C GLY* 2.6 53.1 + - - +
492C THR 5.4 0.3 + - - -
493C ILE* 3.6 29.1 - - + +
496C PHE* 3.4 67.7 - + + +
497C LEU* 5.2 0.7 - - + -
520C TYR* 4.2 7.8 - - + -
521C ILE* 1.3 77.4 - - - +
523C SER* 1.3 75.3 + - - +
524C GLY* 4.2 1.9 - - - -
527C GLN* 2.8 43.9 + - - -
528C THR 3.6 12.8 - - - -
529C SER* 4.2 2.5 - - - -
301D ALA 5.2 0.5 + - - -
302D VAL* 4.3 4.7 - - + +
305D THR* 4.9 1.9 + - - -
322D LEU* 5.8 1.6 - - + -
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Residues in contact with SER 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU 3.6 2.7 - - - -
159C VAL* 5.2 0.2 - - - -
422C GLU* 5.0 3.6 - - - -
425C LEU* 3.8 23.3 - - - +
521C ILE 4.2 0.4 + - - -
522C TYR* 1.3 77.2 - - - +
524C GLY* 1.3 54.5 + - - +
525C MET* 3.7 15.1 + - - +
526C SER* 2.9 30.7 + - - -
527C GLN* 2.7 34.8 + - - -
528C THR* 2.8 17.0 + - - -
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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