Contacts of the strand formed by residues 325 - 331 (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 325 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C HIS 4.5 5.3 + - - -
224C ARG* 3.1 33.5 + - + +
225C ALA 3.4 15.4 + - - -
323C ASP 3.0 27.7 + - - -
324C LEU* 1.3 88.6 - - - +
326C VAL* 1.3 58.0 + - - +
424C ARG* 3.5 21.5 - - + +
483C PHE* 3.4 17.9 - - + -
486C THR 3.5 6.9 - - - +
487C GLY* 3.2 25.8 - - - +
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Residues in contact with VAL 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ILE* 4.4 4.9 - - + -
225C ALA* 3.2 6.5 - - + +
227C LEU* 3.5 18.4 - - + -
324C LEU* 3.5 34.1 - - + +
325C GLN* 1.3 82.4 - - - +
327C LEU* 1.3 73.2 + - - +
328C VAL* 3.5 18.2 - - + -
418C LEU* 4.1 22.2 - - + -
423C ALA* 4.8 1.8 - - + -
424C ARG 3.0 10.0 + - - +
425C VAL* 3.3 6.8 - - + +
426C TYR* 3.1 23.9 + - - +
483C PHE* 3.5 5.7 - - - -
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Residues in contact with LEU 327 (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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225C ALA 2.9 6.1 + - - -
226C VAL* 3.3 10.4 - - + -
227C LEU 3.0 22.2 + - - -
326C VAL* 1.3 76.2 - - - +
328C VAL* 1.3 84.1 + - - +
426C TYR* 3.8 9.0 - - + +
428C TYR* 3.3 34.8 - - + -
479C TYR 5.5 0.2 - - - -
480C TRP* 3.7 43.7 - - + +
483C PHE* 3.6 34.8 - - + -
489C PRO* 5.2 6.1 - - + -
500C TRP* 4.1 21.1 - - + -
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Residues in contact with VAL 328 (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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227C LEU* 3.6 21.3 - - + +
231C THR* 5.9 0.9 - - + -
326C VAL* 3.5 19.1 - - + -
327C LEU* 1.3 82.4 - - - +
329C GLY* 1.3 63.6 + - - +
411C VAL* 3.2 37.2 - - + +
414C LEU* 4.9 12.8 - - + -
415C ALA* 5.2 7.6 - - + -
418C LEU* 5.4 1.6 - - + -
425C VAL* 4.4 12.1 - - + -
426C TYR 3.0 11.4 + - - +
427C ALA* 3.0 25.6 - - + -
428C TYR* 3.1 11.8 - - - -
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Residues in contact with GLY 329 (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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227C LEU 3.4 5.6 + - - +
229C SER 3.4 14.8 + - - -
328C VAL* 1.3 80.6 - - - +
330C VAL* 1.3 73.4 + - - +
411C VAL* 3.9 8.0 - - - +
427C ALA* 5.4 0.9 - - - -
428C TYR* 3.1 35.9 - - - -
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Residues in contact with VAL 330 (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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229C SER* 4.4 4.9 - - - +
329C GLY* 1.3 83.1 - - - +
331C VAL* 1.3 73.1 + - - +
334C GLU* 3.4 15.9 - - - +
407C VAL* 4.2 1.1 - - + -
408C VAL* 3.7 31.2 - - + -
411C VAL* 3.3 31.4 - - + -
428C TYR* 3.3 11.1 + - - -
429C ILE* 3.3 26.1 - - + -
430C PHE 2.7 31.0 + - - -
524C LEU* 5.2 1.3 - - + -
525C ARG* 6.0 1.8 - - - +
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Residues in contact with VAL 331 (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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229C SER* 3.8 4.2 + - - +
330C VAL* 1.3 92.9 - - - +
332C LYS* 1.3 71.0 + - - +
333C ASP 3.4 0.3 + - - -
334C GLU* 3.0 34.6 + - - +
408C VAL* 5.1 0.7 - - - +
428C TYR* 5.6 0.2 - - + -
429C ILE* 4.5 2.9 - - - +
430C PHE* 3.4 28.5 - - + -
445C VAL* 3.5 27.1 - - + +
446C PRO 3.9 11.7 - - - +
447C HIS* 4.0 4.0 - - - -
450C GLU* 3.7 27.6 - - + +
525C ARG* 5.9 0.3 + - - -
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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