Contacts of the strand formed by residues 643 - 648 (chain A) in PDB entry 1U1H
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 GLN 643 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A LEU* 3.8 14.8 + - - +
423A GLN* 2.9 44.4 + - + +
424A GLN* 5.3 2.0 - - - +
427A LEU* 3.6 22.1 - - + +
429A LEU* 5.7 0.8 - - - +
600A GLY 3.0 9.8 + - - +
601A VAL* 3.2 11.0 - - + +
602A ILE 2.9 24.9 + - - -
641A SER 3.4 2.2 + - - -
642A THR* 1.3 74.3 - - - +
644A ILE* 1.3 63.0 + - - +
645A HIS* 3.3 22.6 + - - +
666A ASP* 3.7 9.2 - - + -
667A VAL* 3.9 10.8 - - + +
728A TRP* 3.5 19.9 - - - -
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Residues in contact with ILE 644 (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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411A ARG* 4.2 5.4 - - - +
591A VAL* 4.6 4.5 - - + -
602A ILE* 3.3 16.8 - - + +
604A ILE* 4.2 9.0 - - + -
631A PHE* 4.6 8.1 - - + -
635A ASN* 3.1 58.8 - - + +
638A VAL* 3.5 27.8 - - + -
642A THR* 4.2 9.6 - - + +
643A GLN* 1.3 78.5 - - - +
645A HIS* 1.3 68.5 + - - +
665A ALA* 4.0 6.2 - - + +
666A ASP* 2.6 40.3 + - - +
667A VAL 3.3 5.6 + - - +
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Residues in contact with HIS 645 (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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435A THR* 5.7 0.6 - - + +
485A VAL* 5.5 0.2 - - - +
555A LYS* 4.3 19.0 + - - -
601A VAL* 3.3 30.6 - - + +
602A ILE 2.9 8.4 + - - +
603A GLN* 3.8 21.5 - - + +
604A ILE* 2.5 35.9 + - - +
643A GLN* 3.3 20.6 + - + +
644A ILE* 1.3 80.1 - - - +
646A THR* 1.3 56.3 + - - +
665A ALA* 5.0 0.2 - - - -
667A VAL* 3.1 43.5 + - + +
668A ILE* 5.8 0.4 - - - -
669A THR* 6.1 4.4 - - + +
728A TRP* 3.7 23.5 - + - -
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Residues in contact with THR 646 (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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604A ILE 2.8 13.5 + - - -
606A GLU 4.3 3.1 + - - -
631A PHE* 3.6 18.1 - - - -
645A HIS* 1.3 75.2 - - - +
647A HIS* 1.3 64.6 + - - +
648A MSE 4.2 8.0 - - + +
663A MSE 3.2 30.3 - - + +
665A ALA* 3.6 9.6 - - + -
667A VAL 3.0 7.1 + - - -
668A ILE* 3.2 29.4 - - + +
669A THR* 3.1 24.1 + - - +
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Residues in contact with HIS 647 (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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437A ILE* 3.4 28.4 - - + +
603A GLN* 4.0 12.9 - - - +
604A ILE 3.2 7.5 + - - -
605A ASP* 3.3 13.7 - - + +
606A GLU 2.7 32.6 + - - -
607A ALA 3.9 0.3 + - - -
645A HIS 4.3 0.2 - - - -
646A THR* 1.3 71.2 - - - +
648A MSE 1.3 72.4 + - - +
649A CYS* 3.8 2.2 - - - -
669A THR* 2.9 38.3 + - + +
670A ILE 5.0 1.8 - - - -
732A ASP 3.6 17.7 - - - -
733A CYS* 3.7 0.4 - - - -
766A ZN 2.2 35.1 - - - -
772A MET* 3.4 20.0 - - + -
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Residues in contact with MSE 648 (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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606A GLU* 3.7 21.5 - - + +
609A LEU* 3.8 17.7 - - + -
646A THR* 4.2 13.0 - - + +
647A HIS* 1.3 83.8 - - - +
649A CYS* 1.3 55.4 + - - +
650A TYR* 2.7 28.5 + - + +
653A PHE* 4.4 9.0 - - + -
660A ILE* 3.9 33.7 - - + -
663A MSE 3.7 23.1 - - - +
668A ILE* 4.2 20.9 - - + -
669A THR 3.0 10.4 + - - +
670A ILE* 3.6 32.5 - - + +
671A GLU 3.8 1.0 + - - -
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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