Contacts of the strand formed by residues 401 - 408 (chain A) in PDB entry 1Q6X
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 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A VAL* 4.1 27.4 - - + -
297A LEU* 3.9 26.5 - - + +
300A LEU* 4.1 20.2 - - + -
301A HIS* 3.9 20.6 - - + +
397A ILE 3.1 16.2 + - - +
398A VAL 3.6 10.1 + - - +
399A LYS 3.5 1.7 - - - +
400A ASN* 1.3 76.1 - - - +
402A ASP* 1.3 70.3 + - - +
403A PHE* 3.9 11.7 + - + -
563A GLY* 5.3 0.9 - - - -
564A PRO* 5.2 2.0 - - + -
586A SER* 4.1 18.4 - - - -
587A SER 4.1 5.2 - - - +
588A PHE* 4.9 4.5 - - + -
589A HIS* 3.7 10.0 + - - -
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Residues in contact with ASP 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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400A ASN 3.3 0.2 + - - -
401A LEU* 1.3 72.4 - - - +
403A PHE* 1.3 64.7 + - - +
586A SER* 3.3 3.3 - - - -
587A SER* 2.9 34.6 + - - +
588A PHE 5.7 0.2 - - - -
589A HIS* 3.4 39.8 + - + +
594A THR 4.9 0.9 - - - +
595A SER* 3.9 8.5 + - - -
596A SER* 2.8 49.3 + - - -
597A VAL* 4.7 10.3 + - - +
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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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293A THR* 3.9 18.1 - - + +
296A ALA* 3.4 28.5 - - + -
297A LEU* 3.9 26.9 - - + +
300A LEU* 4.6 10.5 - - + -
401A LEU* 3.8 12.5 + - + -
402A ASP* 1.3 81.6 + - - +
404A ILE* 1.3 75.1 + - - +
405A VAL* 3.5 20.9 - - + -
561A CYS* 3.6 36.8 - - + -
562A TYR 4.9 3.8 - - - -
584A CYS* 3.9 19.1 - - + -
585A ILE 3.4 19.5 - - - -
586A SER* 3.9 14.6 - - - -
596A SER* 4.5 0.4 - - - -
597A VAL* 6.1 0.2 - - - +
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Residues in contact with ILE 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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293A THR* 4.0 9.2 - - + +
403A PHE* 1.3 82.9 - - - +
405A VAL* 1.3 75.9 + - - +
406A TYR* 4.9 10.1 - - + +
583A PHE 3.6 1.6 - - - +
584A CYS* 3.6 1.6 - - - -
585A ILE* 3.0 47.4 + - + +
596A SER* 3.9 24.9 - - - +
597A VAL* 4.4 29.2 - - + -
600A ALA* 4.4 13.5 - - + -
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Residues in contact with VAL 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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292A ASP* 3.8 27.1 - - + +
293A THR* 3.2 29.1 + - - +
403A PHE* 3.5 24.9 - - + -
404A ILE* 1.3 78.4 - - - +
406A TYR* 1.3 59.4 + - - +
407A LYS* 3.9 21.5 + - - -
559A PHE* 4.0 16.8 - - + -
582A THR* 4.1 17.9 - - + -
583A PHE 3.6 3.1 - - - -
584A CYS* 4.4 4.5 - - - +
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Residues in contact with TYR 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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404A ILE* 3.7 13.2 + - + -
405A VAL* 1.3 72.5 - - - +
407A LYS* 1.3 67.2 + - - +
408A PHE* 3.7 27.2 + - + -
582A THR* 3.7 0.6 - - - -
583A PHE* 2.7 61.9 + + + +
585A ILE* 5.1 0.4 - - + -
600A ALA* 3.7 46.1 + - + -
601A GLU* 4.6 12.0 + - + -
603A VAL* 5.3 1.3 - - + -
604A GLY* 3.5 24.3 - - - -
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Residues in contact with LYS 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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292A ASP* 2.5 39.2 + - - +
405A VAL* 3.9 24.9 + - - -
406A TYR* 1.3 81.9 - - - +
408A PHE* 1.3 63.5 + - - +
409A ASP* 3.5 13.1 + - + +
580A ALA* 5.9 4.5 - - + -
581A ILE 3.9 2.5 - - - +
582A THR* 3.7 24.0 - - - +
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Residues in contact with PHE 408 (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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406A TYR* 3.7 19.1 + - + -
407A LYS* 1.3 72.0 - - - +
409A ASP* 1.3 57.7 + - - +
410A ASN* 3.3 31.6 - - + -
411A TYR* 3.5 51.1 - + - -
580A ALA* 3.3 6.2 - - - +
581A ILE* 2.9 50.8 + - + +
583A PHE* 4.4 6.5 - - + -
604A GLY* 4.0 20.9 - - - -
607A LEU* 3.4 45.5 - - + -
608A VAL* 4.2 5.4 - - + -
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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