Contacts of the helix formed by residues 640 - 650 (chain A) in PDB entry 2P6U
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 640 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A LEU* 3.1 29.8 - - + +
635A VAL* 3.5 6.4 + - - +
637A ILE* 2.8 35.0 - - + +
639A HIS* 1.3 73.5 - - - +
641A GLY* 1.3 55.6 + - - +
644A ARG* 3.2 24.9 - - + +
645A ALA* 4.3 7.0 - - + +
648A LEU* 5.3 5.6 - - + -
659A ILE* 3.9 22.4 - - + -
670A ILE* 4.9 9.0 - - + -
678A VAL* 4.1 12.1 - - + -
704A PO4 2.5 29.7 + - - -
709A PO4 2.9 25.1 + - - +
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Residues in contact with GLY 641 (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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625A HIS* 5.7 2.0 - - - -
635A VAL* 4.1 11.2 - - - +
639A HIS* 3.5 13.1 - - - -
640A ILE* 1.3 76.7 - - - +
642A ARG* 1.3 61.6 + - - -
645A ALA* 2.8 35.2 + - - +
704A PO4 2.9 21.5 + - - -
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Residues in contact with ARG 642 (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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570A TRP* 3.5 42.6 + - - -
573A GLU* 3.3 26.4 + - + +
574A LYS 2.4 30.7 + - - +
575A ASP* 4.9 1.0 - - - +
576A GLU* 3.5 28.5 + - - +
579A ILE* 4.2 2.8 - - - +
625A HIS 2.7 28.0 + - - +
626A GLY 2.8 21.1 + - - +
627A VAL* 3.8 15.4 - - + +
631A LEU* 4.1 1.7 - - - +
641A GLY* 1.3 70.4 - - - +
643A VAL* 1.3 73.8 + - + +
645A ALA* 3.6 0.7 - - - +
646A ARG* 2.8 27.0 + - - +
704A PO4 3.5 5.5 + - - +
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Residues in contact with VAL 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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641A GLY 3.3 0.4 - - - -
642A ARG* 1.3 87.5 - - + +
644A ARG* 1.3 68.7 + - + +
646A ARG* 3.0 11.9 + - - +
647A LYS* 3.2 21.3 + - + +
704A PO4 3.3 22.3 + - - +
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Residues in contact with ARG 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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640A ILE* 3.2 21.7 + - + +
643A VAL* 1.3 76.7 - - + +
645A ALA* 1.3 63.2 + - - +
646A ARG 3.2 0.3 + - - -
647A LYS* 3.2 9.7 + - - +
648A LEU* 2.9 28.4 + - - +
670A ILE* 3.3 36.1 - - + +
674A ILE* 3.2 21.9 - - - +
704A PO4 2.8 27.1 + - - +
705A PO4 3.2 33.4 + - - -
709A PO4 2.6 54.8 + - - -
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Residues in contact with ALA 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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631A LEU* 3.5 21.3 - - + -
634A LEU* 3.3 29.2 - - + +
635A VAL* 3.9 19.1 - - + +
640A ILE* 4.2 5.7 + - + +
641A GLY 2.8 25.7 + - - +
642A ARG 3.6 0.9 - - - +
644A ARG* 1.3 73.0 - - - +
646A ARG* 1.3 57.3 + - - +
648A LEU* 4.6 1.3 - - - -
649A TYR* 2.8 26.2 + - - +
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Residues in contact with ARG 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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573A GLU* 3.1 29.6 + - - +
628A LYS* 3.7 17.8 - - - +
630A GLU* 2.7 31.3 + - - -
631A LEU* 2.8 28.9 - - + +
642A ARG 2.8 16.3 + - - +
643A VAL* 3.4 9.9 - - - +
645A ALA* 1.3 70.1 - - - +
647A LYS* 1.3 56.3 + - - +
649A TYR* 2.9 17.7 + - - +
650A ASN* 2.6 64.8 + - - +
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Residues in contact with LYS 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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643A VAL* 3.2 18.3 + - + +
644A ARG* 3.5 10.3 - - - +
646A ARG* 1.3 80.1 - - - +
648A LEU* 1.3 69.1 + - + +
650A ASN* 3.1 16.0 + - - +
651A ALA* 3.3 12.3 + - - +
668A SER 4.7 1.8 + - - -
669A LEU* 2.7 55.7 + - + +
670A ILE* 5.7 1.6 - - + -
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Residues in contact with LEU 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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634A LEU* 4.0 8.3 - - + -
640A ILE* 5.3 5.4 - - + -
644A ARG* 2.9 20.3 + - + +
645A ALA* 3.7 5.2 - - - +
647A LYS* 1.3 77.6 - - + +
649A TYR* 1.3 57.8 + - - +
651A ALA* 3.2 10.6 + - - +
653A ILE* 2.3 58.3 + - + +
659A ILE* 4.0 20.4 - - + -
666A VAL* 4.1 8.1 - - + -
669A LEU* 4.0 22.9 - - + -
670A ILE* 3.4 42.6 - - + -
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Residues in contact with TYR 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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630A GLU* 3.2 63.8 + - + +
631A LEU* 4.4 2.0 - - + -
634A LEU* 4.0 7.2 - - + -
645A ALA 2.8 19.6 + - - +
646A ARG* 3.5 25.4 - - - +
648A LEU* 1.3 73.2 - - - +
650A ASN* 1.3 62.2 + - - +
651A ALA 2.7 19.1 + - - +
653A ILE 3.5 3.6 - - - -
654A ARG* 3.0 71.6 + - + -
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Residues in contact with ASN 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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646A ARG* 2.6 55.6 + - - +
647A LYS* 3.1 9.8 + - - +
649A TYR* 1.3 76.4 + - - +
651A ALA* 1.3 57.2 + - - +
654A ARG* 5.3 3.3 + - - +
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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