Contacts of the strand formed by residues 396 - 401 (chain A) in PDB entry 1YGS
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 ASP 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A GLU 3.4 0.3 - - - +
391A CYS* 3.1 5.7 - - - -
392A LYS* 2.7 52.8 + - + +
395A GLY* 1.3 76.7 - - - +
397A VAL* 1.3 59.0 + - - +
398A TRP* 4.5 6.9 + - - +
436A LYS* 3.4 24.3 + - - +
438A PHE 3.7 10.5 - - - +
439A ASP* 3.3 9.3 - - - +
440A LEU* 3.0 26.9 + - - +
441A ARG 4.9 0.5 + - - -
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Residues in contact with VAL 397 (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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323A TRP* 3.7 35.4 - - + -
389A LEU* 4.9 6.1 - - + -
390A GLU 3.2 8.5 - - - +
391A CYS* 4.8 0.2 - - - -
395A GLY* 3.8 11.2 + - - +
396A ASP* 1.3 76.9 - - - +
398A TRP* 1.3 68.9 + - - +
399A VAL* 5.3 1.3 - - + -
436A LYS* 3.6 2.6 - - - -
437A VAL* 2.7 34.5 + - + +
438A PHE* 3.1 32.6 + - + +
501A LEU* 3.9 18.4 - - + -
527A ILE* 6.2 0.4 - - + -
529A LEU* 4.0 16.8 - - + -
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Residues in contact with TRP 398 (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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388A GLN 3.7 0.3 - - - +
389A LEU* 3.5 4.5 - - - -
390A GLU* 2.8 37.9 + - + +
392A LYS* 3.4 44.6 - - + +
396A ASP* 4.5 4.6 + - - +
397A VAL* 1.3 88.7 - - - +
399A VAL* 1.3 61.2 + - - +
434A TYR* 3.6 57.7 - + + +
435A ILE* 3.3 8.5 - - - -
436A LYS* 3.4 48.0 - - + +
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Residues in contact with VAL 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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387A VAL* 4.3 8.7 - - + -
388A GLN 3.4 6.3 - - - +
389A LEU* 3.8 18.2 - - + -
397A VAL* 5.3 1.1 - - + -
398A TRP* 1.3 74.6 - - - +
400A ARG* 1.3 72.2 + - - +
401A CYS 4.4 1.6 - - - +
407A VAL* 5.2 1.8 - - + -
409A VAL* 4.9 2.0 - - + -
429A ILE* 4.1 18.9 - - + +
433A ALA 3.8 0.9 - - - +
434A TYR* 3.4 4.5 - - - -
435A ILE* 2.7 36.0 + - - +
437A VAL* 3.6 32.9 - - + +
501A LEU* 5.7 1.8 - - + -
503A MET* 3.9 25.4 - - + -
527A ILE* 6.2 0.7 - - + -
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Residues in contact with ARG 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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347A ILE* 5.9 1.4 - - - +
387A VAL* 3.2 7.3 - - - +
388A GLN* 3.0 64.4 + - + +
390A GLU* 4.8 3.8 + - - -
399A VAL* 1.3 76.8 - - - +
401A CYS* 1.3 62.1 + - - +
402A LEU* 3.3 21.4 + - + +
432A SER* 4.8 5.4 + - - +
433A ALA 3.2 9.9 - - - +
434A TYR* 3.4 58.0 - - + +
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Residues in contact with CYS 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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386A GLY 4.2 2.5 - - - -
387A VAL* 4.3 5.6 - - + -
399A VAL* 4.2 2.0 - - + +
400A ARG* 1.3 71.3 - - - +
402A LEU* 1.3 59.9 + - - +
403A SER* 3.9 8.3 - - - -
405A HIS 3.4 25.6 - - - -
407A VAL* 4.2 13.2 - - + -
429A ILE* 3.9 23.5 - - + +
430A TYR 3.3 24.9 - - - +
431A PRO* 3.8 7.0 - - - -
432A SER* 2.7 33.1 + - - -
433A ALA 2.8 9.4 + - - +
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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