Contacts of the strand formed by residues 401 - 408 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 4.1 27.8 - - + -
297B LEU* 3.9 26.1 - - + +
300B LEU* 4.1 20.0 - - + -
301B HIS* 3.9 21.3 - - + +
397B ILE 3.1 16.4 + - - +
398B VAL 3.6 10.7 + - - +
399B LYS 3.5 1.7 - - - +
400B ASN* 1.3 75.2 - - - +
402B ASP* 1.3 69.6 + - - +
403B PHE* 3.8 11.4 + - + -
563B GLY* 5.3 0.4 - - - -
564B PRO* 5.2 2.0 - - + -
586B SER* 4.1 19.1 - - - -
587B SER 4.1 4.7 - - - +
588B PHE* 4.9 5.1 - - + -
589B HIS* 3.7 9.3 - - - -
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Residues in contact with ASP 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B ASN 3.3 0.6 + - - -
401B LEU* 1.3 70.8 - - - +
403B PHE* 1.3 63.5 + - - +
586B SER* 3.3 2.9 - - - -
587B SER* 2.9 35.9 + - - +
589B HIS* 3.4 38.6 + - + +
594B THR 4.9 1.0 - - - +
595B SER* 3.9 8.5 + - - -
596B SER* 2.7 50.2 + - - -
597B VAL* 4.7 9.8 + - - +
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Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B THR* 3.8 18.5 - - + +
296B ALA* 3.4 26.9 - - + -
297B LEU* 3.9 27.6 - - + +
300B LEU* 4.6 9.2 - - + -
401B LEU* 3.8 11.8 + - + -
402B ASP* 1.3 81.5 + - - +
404B ILE* 1.3 76.6 + - - +
405B VAL* 3.5 20.9 - - + -
561B CYS* 3.7 35.9 - - + -
562B TYR 4.9 3.6 - - - -
584B CYS* 3.9 19.1 - - + -
585B ILE 3.4 19.3 - - - -
586B SER* 3.9 13.7 - - - -
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Residues in contact with ILE 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B THR* 4.0 8.5 - - + +
403B PHE* 1.3 84.4 - - - +
405B VAL* 1.3 74.7 + - - +
406B TYR* 4.5 9.9 - - + +
583B PHE 3.6 2.3 - - - +
584B CYS* 3.6 1.6 - - - -
585B ILE* 3.0 47.2 + - + +
596B SER* 3.9 26.0 - - - +
597B VAL* 4.4 30.1 - - + -
600B ALA* 4.4 12.8 - - + -
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ASP* 3.8 27.1 - - + +
293B THR* 3.2 29.7 + - - +
403B PHE* 3.5 25.1 - - + -
404B ILE* 1.3 77.9 - - - +
406B TYR* 1.3 59.7 + - - +
407B LYS* 3.9 21.1 + - - -
559B PHE* 4.0 16.8 - - + -
582B THR* 4.1 18.8 - - + -
583B PHE 3.6 2.9 - - - -
584B CYS* 4.4 4.5 - - - +
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Residues in contact with TYR 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B ILE* 3.7 13.9 + - + -
405B VAL* 1.3 72.5 - - - +
407B LYS* 1.3 67.9 + - - +
408B PHE* 3.7 26.5 + - + -
582B THR* 3.7 0.6 - - - -
583B PHE* 2.7 61.2 + + + +
585B ILE* 5.1 0.4 - - + -
600B ALA* 3.7 46.1 + - + -
601B GLU* 4.6 13.0 + - + -
603B VAL* 5.2 1.6 - - + -
604B GLY* 3.5 23.2 - - - -
607B LEU* 6.1 0.2 - - + -
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Residues in contact with LYS 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ASP* 2.5 40.2 + - - +
405B VAL* 3.9 23.7 + - - +
406B TYR* 1.3 83.5 - - - +
408B PHE* 1.3 61.5 + - - +
409B ASP* 3.5 13.6 + - + +
580B ALA* 5.9 5.2 - - + -
581B ILE 3.9 2.0 - - - +
582B THR* 3.7 23.6 - - + +
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Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B TYR* 3.7 18.7 + - + -
407B LYS* 1.3 70.8 - - - +
409B ASP* 1.3 57.5 + - - +
410B ASN* 3.3 31.0 - - + -
411B TYR* 3.5 50.7 - + - -
580B ALA* 3.4 5.9 - - - +
581B ILE* 2.9 47.9 + - + +
583B PHE* 4.4 8.7 - - + -
604B GLY* 4.0 20.6 - - - -
607B LEU* 3.4 47.1 - - + -
608B VAL* 4.2 6.3 - - + -
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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