Contacts of the strand formed by residues 403 - 407 (chain A) in PDB entry 6A5T
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 ALA 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A TYR* 3.2 28.7 + - + +
393A VAL* 3.9 10.8 - - + +
396A GLY 2.7 21.7 + - - +
397A PRO* 3.0 16.3 - - - +
402A GLY* 1.3 72.6 - - - +
404A LYS* 1.3 65.4 + - - +
405A TYR 4.9 0.7 - - - +
406A VAL* 5.8 0.2 - - + -
416A LEU* 4.8 10.7 - - + +
433A VAL* 4.3 19.3 - - + -
434A GLU 4.1 4.9 - - - -
435A ARG* 4.2 1.8 - - - +
436A HIS* 4.5 0.4 - - - +
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Residues in contact with LYS 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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373A LYS 3.8 17.9 + - - +
374A THR* 3.0 25.2 + - - +
375A LEU 4.4 3.7 - - - +
376A SER* 4.7 9.5 + - - -
397A PRO* 4.5 13.5 - - + +
403A ALA* 1.3 81.7 - - - +
405A TYR* 1.3 92.1 + - + +
415A ASP* 3.9 1.9 - - - +
416A LEU* 3.1 36.2 + - - +
417A ARG* 5.9 7.9 - - + +
434A GLU* 3.1 11.1 + - + +
436A HIS* 4.2 12.6 - - + +
1107B ALA* 4.0 17.0 - - - +
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Residues in contact with TYR 405 (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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403A ALA* 5.8 0.2 - - - -
404A LYS* 1.3 110.0 + - + +
406A VAL* 1.3 62.4 + - - +
407A ILE* 3.8 18.8 - - + -
413A ARG* 4.6 20.2 - - + -
414A ILE 3.9 3.6 - - - -
415A ASP* 3.4 48.0 + - + -
416A LEU* 4.5 1.3 - - - +
417A ARG* 4.0 11.7 + - - -
432A LYS 3.9 0.2 - - - +
433A VAL* 3.1 10.7 - - - +
434A GLU* 2.9 52.8 + - + -
1107B ALA* 6.6 0.2 - - + -
1108B ARG* 3.6 25.9 + - - -
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Residues in contact with VAL 406 (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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393A VAL* 4.3 18.2 - - + -
403A ALA* 5.8 0.7 - - + -
405A TYR* 1.3 74.8 - - - +
407A ILE* 1.3 62.1 - - - +
408A ARG* 5.8 0.2 - - - -
414A ILE* 3.3 47.8 + - + +
416A LEU* 4.2 17.9 - - + +
425A ILE* 4.8 9.2 - - + -
427A LEU* 3.7 28.5 - - + -
431A TRP* 4.0 15.5 - - + -
432A LYS 3.4 8.7 - - - +
433A VAL* 4.2 16.2 - - + -
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Residues in contact with ILE 407 (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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3A GLN* 4.9 8.5 - - - +
405A TYR* 3.8 22.6 - - + +
406A VAL* 1.3 75.7 - - - +
408A ARG* 1.3 76.4 + - - +
411A GLY* 4.5 9.2 - - - -
412A ASP 3.7 12.6 - - - +
413A ARG* 3.7 43.7 - - + +
431A TRP* 3.3 5.8 - - - +
432A LYS* 2.9 52.7 + - + +
434A GLU* 4.8 15.5 - - + +
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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