Contacts of the strand formed by residues 348 - 353 (chain A) in PDB entry 3RT0
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 ARG 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A VAL* 3.9 8.7 - - - +
346A ASP 4.7 2.8 + - - +
347A SER* 1.3 80.7 - - - +
349A ALA* 1.3 64.4 + - - +
350A VAL* 3.9 14.6 - - + -
359A PRO* 4.7 4.9 - - + -
361A SER* 3.5 16.6 - - - +
363A ASP* 3.0 35.9 + - - +
428A ILE 3.8 1.0 - - - +
429A LEU* 3.5 2.4 - - - -
430A ALA 3.2 28.4 + - - +
435A TRP* 3.3 46.0 + - + +
440A ASN* 2.7 43.0 + - - +
356B GLU* 3.3 30.9 + - - +
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A VAL* 3.9 14.1 - - + +
341A VAL* 4.0 26.5 - - + -
348A ARG* 1.3 73.5 - - - +
350A VAL* 1.3 61.0 + - - +
359A PRO* 3.5 1.2 - - - +
360A LEU* 2.7 32.2 + - + -
361A SER* 3.2 9.9 + - - +
427A LEU* 4.5 3.8 - - + -
428A ILE 3.3 4.3 - - - -
429A LEU* 3.8 22.2 - - + -
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ARG* 3.9 9.6 - - - -
349A ALA* 1.3 80.3 - - - +
351A LEU* 1.3 67.0 + - - +
352A PHE 4.1 0.2 + - - -
357A ALA* 3.9 15.3 - - + -
358A MET 3.8 9.0 - - - +
359A PRO* 4.2 4.0 - - + -
426A CYS 4.1 0.5 - - - +
427A LEU* 3.5 5.5 - - - +
428A ILE* 2.8 40.1 + - + +
435A TRP* 3.6 29.2 - - + -
440A ASN* 3.6 24.9 - - + +
444A CYS* 3.4 29.0 - - - -
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ILE* 4.0 10.3 - - + -
350A VAL* 1.3 74.6 - - - +
352A PHE* 1.3 66.5 + - - +
353A ARG* 3.7 34.3 - - + +
356A GLU 3.6 0.7 - - - +
357A ALA* 3.5 1.6 - - - -
358A MET* 2.6 53.0 + - + +
360A LEU* 3.9 19.0 - - + +
418A MET* 4.2 18.6 - - + -
424A ASP* 3.8 20.4 - - + +
426A CYS 3.7 3.6 - - - +
427A LEU* 4.1 4.0 - - + +
501A LEU* 3.4 32.8 - - + -
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Residues in contact with PHE 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A VAL 4.1 0.8 + - - -
351A LEU* 1.3 73.9 - - - +
353A ARG* 1.3 57.5 + - - +
354A GLY 3.8 11.9 - - - -
355A LYS* 3.3 33.0 - - + -
356A GLU 3.5 15.7 - - - -
357A ALA 4.1 0.2 - - - -
424A ASP* 3.6 2.1 - - - -
425A GLU* 2.8 46.3 + - + +
426A CYS* 2.9 24.2 + - - +
441A GLN* 3.9 7.6 - - - -
444A CYS* 3.4 40.6 - - + -
445A GLU* 4.1 19.3 - - + -
448A ARG* 3.7 32.5 - - + -
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Residues in contact with ARG 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ILE* 6.0 0.2 - - - +
351A LEU* 3.7 20.4 + - + +
352A PHE* 1.3 72.1 - - - +
354A GLY* 1.3 69.2 + - - +
355A LYS 3.1 0.5 + - - -
356A GLU* 3.0 27.3 + - - +
358A MET* 4.1 23.9 - - - +
418A MET* 3.8 11.0 - - - +
419A PRO 2.8 24.7 + - - -
420A ARG* 3.8 0.4 - - - +
421A SER* 3.4 18.0 - - - +
423A GLU* 3.9 21.8 - - + +
424A ASP* 2.5 38.5 + - - +
362B VAL* 3.6 27.0 - - - +
365B LYS* 6.3 0.4 - - - +
368B ARG* 3.8 17.4 - - - +
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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