Contacts of the helix formed by residues 656 - 662 (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 ILE 656 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A LEU* 4.5 15.0 - - + -
610A ARG* 3.4 38.8 - - + +
613A LEU* 6.5 0.9 - - + -
624A LEU* 4.4 19.3 - - + -
650A TYR* 6.1 3.1 - - + -
653A PHE* 3.2 32.8 - - + +
654A ASN 3.8 0.4 + - - -
655A ASP* 1.3 79.3 - - - +
657A ILE* 1.3 68.7 + - - +
658A HIS 3.3 2.5 - - - -
659A SER* 3.1 22.8 + - - +
660A ILE* 3.0 28.4 - - + +
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Residues in contact with ILE 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A PHE* 2.6 21.4 + - + +
654A ASN* 4.4 8.5 - - - +
656A ILE* 1.3 77.2 - - - +
658A HIS* 1.3 72.5 + - + +
660A ILE* 2.9 16.8 + - + +
661A ILE* 3.2 18.6 + - + +
682A VAL* 3.8 27.8 - - + +
683A PHE* 3.4 39.5 - - + -
687A VAL* 3.8 25.6 - - + -
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Residues in contact with HIS 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A ILE 3.3 1.0 - - - -
657A ILE* 1.3 87.2 - - + +
659A SER* 1.3 62.6 + - - +
661A ILE* 3.4 20.8 + - + +
662A ASP* 3.0 32.3 + - - +
687A VAL* 6.0 0.8 - - + +
767A ZN 2.1 34.4 - - - -
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Residues in contact with SER 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A LEU* 5.8 1.6 - - - -
624A LEU* 3.5 34.2 + - - +
628A VAL* 3.4 29.1 - - - +
656A ILE* 3.1 22.1 + - - +
657A ILE 3.1 1.0 - - - -
658A HIS* 1.3 77.7 - - - +
660A ILE* 1.3 67.6 + - - +
662A ASP* 3.3 5.5 + - - +
663A MSE 3.3 16.3 + - - +
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Residues in contact with ILE 660 (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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609A LEU* 4.5 9.2 - - + -
648A MSE 3.9 19.3 - - + -
653A PHE* 3.8 25.1 - - + -
656A ILE* 3.0 43.1 - - + +
657A ILE* 2.9 12.8 + - + +
659A SER* 1.3 77.8 - - - +
661A ILE* 1.3 63.7 + - - +
663A MSE 3.0 26.2 - - - +
664A ASP 3.9 1.4 + - - -
665A ALA 5.2 0.7 + - - -
668A ILE* 3.5 35.6 - - + +
683A PHE* 4.3 9.9 - - + -
689A TYR* 4.7 7.2 + - + -
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Residues in contact with ILE 661 (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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657A ILE* 3.2 15.5 + - + +
658A HIS* 3.5 24.2 - - + +
659A SER 3.2 0.2 - - - -
660A ILE* 1.3 72.2 - - + +
662A ASP* 1.3 65.6 + - - +
663A MSE 2.9 4.9 - - - -
664A ASP* 2.8 24.9 + - - +
687A VAL* 3.1 44.9 - - + +
688A LYS 5.4 0.2 - - - +
689A TYR* 3.8 32.2 - - + +
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Residues in contact with ASP 662 (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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410A HIS* 5.4 5.5 + - - -
628A VAL* 3.2 14.2 - - + +
632A ARG* 2.7 43.9 + - - +
658A HIS* 3.0 24.6 + - - +
659A SER* 3.3 8.3 + - - +
661A ILE* 1.3 77.2 - - - +
663A MSE 1.3 56.4 - - - +
664A ASP* 3.2 2.7 + - - +
767A ZN 2.2 36.7 - - - -
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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