Contacts of the strand formed by residues 509 - 513 (chain C) in PDB entry 1C2O
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 GLN 509 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427C ALA* 4.3 1.0 + - - +
501C PRO* 3.9 35.2 - - + +
502C PRO 4.0 7.3 - - - +
503C TYR* 3.2 30.5 + - - +
504C THR* 3.9 9.4 + - - +
507C ALA* 3.5 31.7 - - + +
508C GLN* 1.3 72.9 - - - +
510C TYR* 1.3 61.7 + - - +
520C VAL* 3.5 20.6 - - + +
521C ARG 3.2 5.6 - - - +
522C ARG* 4.9 10.4 - - + +
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Residues in contact with TYR 510 (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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427C ALA* 3.6 28.0 - - + +
428C TYR 4.3 1.6 - - - +
429C ILE* 3.3 35.0 - - + +
500C TRP* 5.5 0.2 - - - +
501C PRO 5.4 1.1 - - - -
503C TYR* 4.8 2.9 - + + -
508C GLN 4.1 4.7 - - - -
509C GLN* 1.3 76.8 - - - +
511C VAL* 1.3 69.0 + - - +
520C VAL* 3.4 3.5 - - - +
521C ARG* 2.7 83.8 + - + +
522C ARG 4.0 3.7 + - - -
523C GLY 3.1 36.8 + - - -
524C LEU* 3.9 19.6 - - + +
525C ARG 5.5 0.3 + - - -
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Residues in contact with VAL 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C ALA 3.1 16.2 + - - +
429C ILE 2.9 24.3 + - - -
500C TRP* 3.5 31.6 - - + -
501C PRO* 3.9 16.6 - - + -
510C TYR* 1.3 87.4 - - - +
512C SER* 1.3 59.3 + - - +
513C LEU* 3.3 19.7 + - + -
518C LEU* 3.4 30.3 - - + -
519C GLU 4.3 0.2 - - - -
520C VAL* 3.9 14.6 - - + +
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Residues in contact with SER 512 (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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429C ILE* 4.1 5.2 - - - +
431C GLU* 3.0 15.9 + - - -
475C ARG* 4.6 0.5 + - - -
511C VAL* 1.3 72.5 - - - +
513C LEU* 1.3 57.4 + - - +
514C ASN* 3.2 22.3 + - - +
516C LYS 4.5 4.0 + - - +
517C PRO 4.5 0.2 - - - +
518C LEU* 3.7 19.5 - - - +
519C GLU* 3.7 23.1 + - - +
521C ARG* 3.2 36.5 + - - +
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Residues in contact with LEU 513 (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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428C TYR* 3.5 24.2 - - + -
429C ILE 3.2 13.9 + - - +
430C PHE* 3.5 16.5 - - + -
431C GLU 3.0 20.4 + - - -
472C PHE* 3.9 11.7 - - + -
475C ARG* 4.9 3.1 - - - +
476C LEU* 3.3 31.0 - - + -
479C TYR* 3.8 26.5 - - + -
480C TRP* 4.7 5.4 - - + -
500C TRP* 3.5 28.7 - - + -
511C VAL* 3.3 13.9 + - + -
512C SER* 1.3 67.6 - - - +
514C ASN* 1.3 64.9 + - - +
518C LEU* 4.1 5.2 - - + -
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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