Contacts of the strand formed by residues 398 - 404 (chain A) in PDB entry 1RS0
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 LEU 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A MET* 4.9 0.2 - - + -
357A HIS* 3.1 22.4 - - + +
359A ILE* 4.5 14.4 - - + -
377A ILE* 4.8 5.8 - - + -
380A ILE* 4.2 15.9 - - + -
381A ARG* 3.8 35.9 - - + +
384A LEU* 4.5 6.5 - - + -
386A ILE* 3.4 19.7 - - + +
395A GLU* 3.1 6.3 + - - +
396A ASP 3.4 1.2 - - - -
397A TYR* 1.3 80.5 - - - +
399A ASP* 1.3 73.2 + - - +
400A VAL* 4.2 19.1 - - + -
419A SER* 4.2 2.3 + - - +
421A LYS* 2.6 34.1 + - - -
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Residues in contact with ASP 399 (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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357A HIS 2.9 9.0 + - - +
358A VAL* 3.4 16.3 - - + +
359A ILE* 2.7 33.8 + - - +
396A ASP* 4.2 9.9 - - - +
398A LEU* 1.3 81.4 - - - +
400A VAL* 1.3 59.3 + - - +
401A TYR* 3.8 26.6 + - + -
419A SER* 3.4 4.7 - - - -
421A LYS* 3.0 19.8 + - - +
424A GLU* 4.9 3.1 - - - +
426A HIS* 3.2 18.7 + - - +
443A MET* 6.1 0.7 - - - -
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Residues in contact with VAL 400 (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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334A LEU* 5.8 1.3 - - + -
359A ILE* 3.6 20.0 - - + -
361A LEU* 5.7 2.5 - - + -
377A ILE* 4.1 31.0 - - + -
398A LEU* 4.2 22.2 - - + -
399A ASP* 1.3 75.6 - - - +
401A TYR* 1.3 61.7 + - - +
402A VAL* 4.5 9.2 - - + -
417A LEU* 3.3 29.6 - - + +
418A ALA* 3.2 8.3 - - - +
419A SER* 2.7 43.4 + - - +
426A HIS* 3.6 5.3 - - - +
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Residues in contact with TYR 401 (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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358A VAL* 3.7 17.3 - - + -
359A ILE 2.7 12.8 + - - +
360A ILE* 4.4 11.4 - - + -
361A LEU* 2.8 27.1 + - - +
399A ASP* 3.8 25.4 + - + -
400A VAL* 1.3 75.1 - - - +
402A VAL* 1.3 63.6 + - - +
403A PHE* 4.1 12.8 - + + -
424A GLU* 4.4 0.9 + - - -
425A GLN 3.6 13.0 - - - -
426A HIS* 3.4 38.7 + + - +
439A VAL* 3.3 32.5 - - + -
442A GLN* 3.3 29.6 + - - +
443A MET* 3.6 25.3 + - + +
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Residues in contact with VAL 402 (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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361A LEU* 3.3 20.0 - - + +
363A THR* 4.4 13.9 - - + -
400A VAL* 4.5 4.0 - - + -
401A TYR* 1.3 79.1 - - - +
403A PHE* 1.3 65.7 + - - +
404A GLY 3.8 0.7 + - - -
414A ILE* 3.4 56.3 - - + +
417A LEU* 4.4 11.4 - - + -
418A ALA* 4.0 19.5 - - + +
426A HIS 3.0 7.7 + - - +
427A VAL* 3.5 5.0 - - - +
428A CYS 3.2 23.2 + - - +
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Residues in contact with PHE 403 (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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267A VAL* 4.3 11.4 - - + -
268A LEU* 5.3 0.4 - - + -
271A LEU* 5.2 7.0 - - + -
360A ILE* 3.7 31.0 - - + -
361A LEU 2.8 8.8 + - - -
362A MET* 3.4 29.1 - - + -
363A THR 3.3 19.0 + - - -
401A TYR* 4.1 17.9 - + + -
402A VAL* 1.3 80.8 - - - +
404A GLY* 1.3 65.3 + - - +
405A VAL* 3.2 5.5 + - - +
426A HIS 5.1 0.9 - - - -
428A CYS* 3.2 12.6 - - + +
430A VAL* 3.8 15.0 - - + -
436A LEU* 3.6 33.7 - - + -
439A VAL* 4.2 28.7 - - + -
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Residues in contact with GLY 404 (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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363A THR 3.3 9.6 - - - -
402A VAL 3.8 2.6 + - - -
403A PHE* 1.3 70.2 - - - +
405A VAL* 1.3 60.9 + - - -
406A GLY 4.0 2.8 + - - +
409A VAL* 4.1 6.6 - - - +
414A ILE* 3.5 21.7 - - - +
428A CYS 2.9 13.4 + - - -
429A LYS* 3.8 12.7 - - - +
430A VAL* 3.1 24.7 + - - +
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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