Contacts of the strand formed by residues 420 - 425 (chain C) in PDB entry 1TYE
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 SER 420 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C GLY 2.6 26.6 + - - -
21C PHE 3.5 19.1 - - - -
22C SER* 4.0 10.3 - - - -
23C LEU* 3.9 12.9 - - - +
418C GLY 3.2 0.4 - - - +
419C PHE* 1.3 79.0 - - - +
421C LEU* 1.3 65.4 + - - +
436C ILE 4.1 0.2 - - - +
437C VAL* 3.6 3.6 - - - +
438C GLY* 2.9 36.7 + - - +
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Residues in contact with LEU 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.9 2.2 - - - +
359C ALA* 3.7 29.9 - - + +
361C ALA* 3.3 21.2 - - + +
375C ALA* 3.8 23.3 - - + +
376C VAL 4.1 1.1 - - - -
377C ALA* 3.8 12.6 - - + +
389C VAL* 3.9 16.4 - - + -
418C GLY 3.9 11.4 - - - +
419C PHE 4.3 0.6 + - - -
420C SER* 1.3 80.3 - - - +
422C ARG* 1.3 80.7 + - - +
435C LEU* 4.6 3.8 - - + -
436C ILE 3.7 2.9 - - - +
437C VAL* 3.5 37.5 - - + -
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Residues in contact with ARG 422 (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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23C LEU* 2.7 47.2 + - + +
24C ASP* 2.9 38.6 + - - +
25C PHE* 3.6 16.7 - - + -
97C VAL 4.9 3.4 + - - -
361C ALA* 3.7 6.6 - - - +
362C PRO* 5.9 4.1 - - - +
421C LEU* 1.3 87.4 + - - +
423C GLY* 1.3 69.7 + - - +
435C LEU* 3.3 7.7 - - - +
436C ILE* 2.9 44.0 + - + +
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Residues in contact with GLY 423 (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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25C PHE* 3.6 12.9 - - - -
361C ALA* 4.4 2.4 - - - +
362C PRO 3.8 12.4 + - - +
363C LEU* 4.2 9.0 - - - -
422C ARG* 1.3 83.9 - - - +
424C ALA* 1.3 71.1 + - - +
425C VAL* 3.3 8.3 + - - +
434C ASP 3.2 14.8 - - - -
435C LEU* 4.3 0.4 - - - +
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Residues in contact with ALA 424 (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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362C PRO* 3.7 11.0 - - + +
363C LEU* 3.7 5.1 - - - +
364C GLY* 3.4 36.5 - - - +
423C GLY* 1.3 75.3 - - - +
425C VAL* 1.3 63.1 + - + +
433C PRO* 4.1 9.8 - - - +
434C ASP 3.5 6.7 + - - -
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Residues in contact with VAL 425 (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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25C PHE* 3.5 54.8 - - + -
33C VAL* 4.1 17.3 - - + -
423C GLY 3.3 3.5 - - - +
424C ALA* 1.3 86.2 - - + +
426C ASP* 1.3 70.1 + - - +
427C ILE 3.2 6.2 + - - -
433C PRO* 4.2 3.8 - - - +
434C ASP* 3.1 23.9 + - - +
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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