Contacts of the helix formed by residues 642 - 651 (chain A) in PDB entry 3JUE
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 GLY 642 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612A ILE* 4.7 0.4 - - - -
634A ASN* 4.5 4.5 - - - -
635A GLN 4.4 0.9 - - - -
636A ALA* 3.9 12.9 - - - +
640A GLY 3.6 3.2 + - - -
641A ARG* 1.3 72.3 - - - +
643A PRO* 1.3 77.3 - - - +
644A LEU 3.2 3.4 - - - -
645A HIS* 3.0 16.3 + - - -
646A HIS* 3.0 24.5 + - - -
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Residues in contact with PRO 643 (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 THR* 5.3 0.4 - - - +
611A LEU* 3.8 27.6 - - + -
612A ILE* 4.4 15.9 - - + -
615A THR* 3.9 6.1 - - - +
632A ASN 4.6 1.3 - - - +
633A VAL 3.2 29.4 - - - +
634A ASN* 4.3 1.3 - - - -
635A GLN 3.3 17.9 - - - +
642A GLY* 1.3 84.0 - - - +
644A LEU* 1.3 56.3 + - - +
646A HIS* 3.3 4.2 + - + +
647A ALA 2.9 23.7 + - - -
659A PHE* 3.3 36.0 - - + -
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Residues in contact with LEU 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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633A VAL 4.9 1.6 + - - +
642A GLY 3.2 0.6 - - - -
643A PRO* 1.3 76.6 - - - +
645A HIS* 1.3 63.5 + - - +
647A ALA* 3.2 2.8 + - - +
648A THR* 2.8 31.8 + - + +
656A ALA* 4.0 36.6 - - + +
659A PHE* 3.8 8.8 - - + -
660A LEU* 4.0 20.6 - - + -
664A ALA* 3.9 28.3 - - + -
665A ASP 3.9 15.0 - - - +
666A LEU* 4.5 1.8 - - - -
676A PRO* 3.7 27.6 - - + -
688A ILE* 6.0 0.2 - - + -
692A LEU* 4.4 11.4 - - + -
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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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640A GLY 3.8 13.2 - - - -
641A ARG* 3.8 15.0 - - + -
642A GLY* 3.0 29.1 + - - +
644A LEU* 1.3 78.5 - - + +
646A HIS* 1.3 57.7 + - - +
648A THR* 3.2 8.6 - - - +
649A ILE* 2.9 34.7 + - + +
665A ASP 5.8 0.2 - - - -
668A ALA* 3.0 42.9 + - + -
670A ASP* 3.8 8.8 + - + -
674A ARG 3.1 16.1 + - - -
676A PRO* 3.7 16.0 - - + +
679A ILE* 3.5 26.8 - - + +
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Residues in contact with HIS 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ILE* 3.8 33.5 - - + +
615A THR* 3.8 16.6 - - + -
616A ALA* 5.6 2.5 - - + +
637A ASP* 2.9 28.0 + - - -
641A ARG* 3.3 37.3 + - + +
642A GLY 3.0 27.9 + - - -
643A PRO* 3.3 6.3 + - + +
644A LEU 3.2 0.2 - - - -
645A HIS* 1.3 72.4 - - - +
647A ALA* 1.3 67.3 + - - +
649A ILE* 3.4 10.9 + - - +
650A LEU* 3.0 35.8 + - + +
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Residues in contact with ALA 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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615A THR* 3.6 7.8 - - - +
643A PRO 2.9 17.3 + - - +
644A LEU 3.7 4.5 - - - +
646A HIS* 1.3 76.1 - - - +
648A THR* 1.3 57.6 + - - +
650A LEU 3.4 0.7 + - - -
651A GLY 3.0 7.1 + - - -
652A HIS* 2.8 37.7 + - - +
655A LEU* 4.1 4.7 - - + -
656A ALA* 3.7 33.2 - - + +
659A PHE* 4.0 11.0 - - + -
688A ILE* 4.7 1.1 - - - -
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Residues in contact with THR 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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644A LEU* 2.8 29.2 + - + +
645A HIS* 3.2 17.9 - - - +
647A ALA* 1.3 75.5 - - - +
649A ILE* 1.3 63.6 + - - +
651A GLY* 3.2 10.6 + - - -
656A ALA* 5.6 0.7 - - - -
676A PRO* 3.6 35.3 + - + +
679A ILE* 3.7 8.7 - - + +
680A ALA* 3.6 17.3 + - - -
683A THR* 4.3 10.4 + - - -
685A ASN* 4.9 1.0 + - - -
688A ILE* 3.9 28.4 - - - +
692A LEU* 5.2 0.2 - - - -
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Residues in contact with ILE 649 (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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641A ARG* 4.1 31.0 - - - +
645A HIS* 2.9 31.9 + - + +
646A HIS* 3.7 14.8 - - - +
648A THR* 1.3 74.0 - - - +
650A LEU* 1.3 74.9 + - + +
651A GLY 3.5 0.2 + - - -
674A ARG* 4.5 14.4 - - - +
679A ILE* 3.7 24.4 - - + +
683A THR* 4.5 11.2 - - + +
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Residues in contact with LEU 650 (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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615A THR* 4.0 3.8 - - + +
616A ALA* 3.7 35.9 - - + +
646A HIS* 3.0 27.5 + - + +
647A ALA 4.2 0.4 - - - +
648A THR 3.2 0.2 - - - -
649A ILE* 1.3 89.6 - - + +
651A GLY* 1.3 62.6 + - - +
652A HIS* 3.4 33.4 + - + +
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Residues in contact with GLY 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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647A ALA 3.0 4.9 + - - -
648A THR 3.2 8.5 + - - -
649A ILE 3.3 1.0 + - - -
650A LEU* 1.3 78.7 - - - +
652A HIS* 1.3 62.4 + - - +
653A THR* 3.3 10.3 + - - -
685A ASN* 3.7 23.2 + - - -
688A ILE* 4.1 4.5 - - - -
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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