Contacts of the strand formed by residues 373 - 379 (chain C) in PDB entry 3DLX
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 ILE 373 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LYS* 6.0 3.4 - - - -
347C VAL* 3.6 31.0 - - + -
349C GLY 3.4 8.7 - - - +
350C LEU* 4.8 0.2 - - + -
351C GLY* 3.9 0.7 - - - +
363C LEU* 4.1 15.0 - - + +
372C THR* 1.3 84.1 + - - +
374C LEU* 1.3 66.7 + - - +
375C PRO* 4.2 1.6 - - - +
377C ALA* 3.5 14.1 - - + -
379C PHE* 3.5 36.3 - - + -
256D PRO* 3.8 19.7 - - + -
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Residues in contact with LEU 374 (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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338C THR* 6.1 4.3 - - + -
339C VAL 5.2 9.0 - - - +
349C GLY* 2.9 16.7 + - - +
350C LEU 3.7 16.4 - - - +
351C GLY* 3.7 21.5 - - - -
352C PRO* 4.2 10.5 - - + -
372C THR* 5.4 0.2 - - - +
373C ILE* 1.3 78.6 - - - +
375C PRO* 1.4 84.3 - - + +
377C ALA* 3.0 20.8 + - - +
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Residues in contact with PRO 375 (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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373C ILE 4.5 1.6 - - - +
374C LEU* 1.4 100.0 - - + +
376C GLY* 1.3 60.4 + - - +
218D ALA* 5.7 0.5 - - - +
251D ILE* 3.5 23.9 - - + +
252D GLY* 5.4 3.6 - - - +
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Residues in contact with GLY 376 (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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348C LEU 4.8 0.3 - - - +
374C LEU 3.3 0.2 + - - -
375C PRO* 1.3 71.7 - - - +
377C ALA* 1.3 63.5 + - - +
378C SER* 4.0 0.9 + - - -
216D ASP* 4.5 3.1 - - - -
218D ALA* 4.8 2.5 - - - -
220D ASN* 2.8 33.2 + - - +
251D ILE* 3.3 20.2 - - - +
252D GLY* 4.5 7.3 - - - +
259D ILE* 4.9 1.6 - - - -
263D GLN* 3.9 12.2 + - - -
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Residues in contact with ALA 377 (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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348C LEU 3.1 16.8 - - - +
349C GLY* 3.6 11.2 - - - +
373C ILE* 3.5 33.9 - - + -
374C LEU 3.0 18.0 + - - +
375C PRO 3.4 0.6 + - - -
376C GLY* 1.3 80.0 + - - +
378C SER* 1.3 60.8 + - - +
256D PRO* 3.2 21.1 - - - +
259D ILE* 3.5 6.2 - - - +
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Residues in contact with SER 378 (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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347C VAL* 3.5 5.7 - - - +
348C LEU* 2.9 36.6 + - - +
376C GLY 5.0 0.3 + - - -
377C ALA* 1.3 74.9 - - - +
379C PHE* 1.3 69.5 + - - +
380C PHE* 3.7 9.0 - - - -
220D ASN* 4.5 3.0 + - - -
256D PRO* 3.3 12.6 - - - -
259D ILE* 3.9 25.1 - - - -
262D PRO* 3.7 24.7 - - - +
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Residues in contact with PHE 379 (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 LYS* 3.4 54.1 - - + +
226C SER 3.6 7.4 - - - -
228C ARG* 3.9 21.3 + - - +
346C GLY 3.2 14.8 - - - +
347C VAL* 3.8 15.5 - - + -
363C LEU* 3.6 26.7 - - + -
373C ILE* 3.5 25.1 - - + -
378C SER* 1.3 75.6 - - - +
380C PHE* 1.3 68.0 + - - +
256D PRO* 3.0 57.9 + - + +
257D GLU* 3.9 9.7 - - + +
259D ILE 5.1 5.0 - - - +
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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