Contacts of the helix formed by residues 650 - 656 (chain A) in PDB entry 1UUR
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 THR 650 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577A ARG* 4.0 31.2 - - + +
578A HIS* 3.6 12.5 + - + +
644A THR* 4.0 6.7 - - + -
645A ALA 4.5 1.8 - - - +
646A ALA 4.8 3.1 - - - +
647A ALA 3.6 22.4 - - - +
649A LYS* 1.3 82.2 - - - +
651A PHE* 1.3 70.1 + - - +
652A PRO* 3.0 24.1 - - - +
653A ASP* 2.6 27.6 + - - +
654A PHE 3.2 7.8 + - - -
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Residues in contact with PHE 651 (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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576A GLN* 4.3 8.9 + - - +
577A ARG 5.0 1.5 + - - +
579A ILE* 3.7 30.1 - - + -
582A LEU* 4.1 6.5 - - + -
588A ILE* 3.7 24.5 - - + -
611A ILE* 3.5 41.3 - - + -
621A PHE* 4.0 15.7 - + + -
623A ILE* 4.7 4.3 - - + -
639A VAL* 4.1 31.4 - - + -
644A THR* 3.5 13.9 + - - +
650A THR* 1.3 73.0 - - - +
652A PRO* 1.3 66.9 - - + +
654A PHE* 3.6 9.9 + + - +
655A LEU* 3.2 39.9 + - + +
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Residues in contact with PRO 652 (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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577A ARG 4.6 0.4 - - - +
578A HIS* 3.7 21.3 - - + -
582A LEU* 4.1 15.5 - - + -
650A THR* 3.0 23.3 - - - +
651A PHE* 1.3 93.2 - - + +
653A ASP* 1.3 65.0 + - - +
655A LEU* 3.5 6.1 + - + -
656A SER* 3.2 14.4 + - - -
686A LEU* 3.2 39.6 - - + +
689A PHE* 4.0 19.5 - - + +
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Residues in contact with ASP 653 (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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648A LYS 2.6 25.2 - - - +
649A LYS* 3.8 11.9 - - + -
650A THR* 2.6 32.7 + - - +
652A PRO* 1.3 73.1 - - - +
654A PHE* 1.3 64.3 + - - +
656A SER* 2.9 23.3 + - - -
657A GLU* 3.4 19.9 + - - +
689A PHE 5.1 7.1 - - - +
691A PRO* 5.1 11.1 - - - +
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Residues in contact with PHE 654 (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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623A ILE* 3.9 24.0 - - + -
637A TYR* 3.6 27.4 - + - -
639A VAL* 4.4 11.7 - - + -
643A ASP* 3.5 40.8 - - + +
644A THR* 5.1 0.9 - - - +
649A LYS* 3.5 29.0 - - + +
650A THR 3.2 2.6 + - - +
651A PHE* 3.6 17.3 - + - +
653A ASP* 1.3 79.7 - - - +
655A LEU* 1.3 67.2 + - + +
657A GLU* 3.2 12.8 + - - +
658A HIS* 3.2 47.6 - + - -
661A PHE* 3.9 10.3 - + - -
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Residues in contact with LEU 655 (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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582A LEU* 5.6 0.7 - - + -
587A ILE* 5.5 4.3 - - + -
609A PHE* 4.4 13.2 - - + -
611A ILE* 3.8 20.9 - - + -
623A ILE* 3.7 29.8 - - + -
651A PHE* 3.2 45.2 + - + +
652A PRO* 3.7 13.0 - - + +
653A ASP 3.0 0.6 + - - -
654A PHE* 1.3 82.7 - - + +
656A SER* 1.3 51.2 + - - +
657A GLU 3.1 2.0 + - - -
658A HIS 3.7 3.8 + - - -
661A PHE* 3.8 20.6 - - + +
682A LYS* 2.8 29.5 + - + -
686A LEU* 4.1 17.3 - - + -
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Residues in contact with SER 656 (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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652A PRO 3.2 10.8 + - - -
653A ASP* 2.9 15.8 + - - -
655A LEU* 1.3 75.8 - - - +
657A GLU* 1.3 60.6 + - - +
658A HIS 3.5 0.9 - - - -
682A LYS* 2.9 21.8 + - - +
683A ASP* 4.6 11.4 - - - +
686A LEU* 4.2 11.7 - - - +
690A ALA* 5.6 2.5 - - - -
691A PRO* 4.6 16.9 - - - +
706A ASN* 4.5 7.1 + - - +
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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