Contacts of the helix formed by residues 608 - 619 (chain A) in PDB entry 1R4X
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 608 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605A HIS* 5.3 1.3 - - - +
606A HIS 4.3 6.3 - - - +
607A MET* 1.3 77.1 - - - +
609A ARG* 1.3 66.4 + - - +
610A GLN* 3.6 8.2 + - - +
611A GLU* 3.0 37.0 + - - +
612A ILE* 3.0 24.7 + - - +
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Residues in contact with ARG 609 (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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608A THR* 1.3 72.3 - - - +
610A GLN* 1.3 59.2 + - - +
612A ILE* 3.4 11.3 + - - +
613A PHE* 3.0 61.4 + - + -
632A SER* 3.7 11.1 + - - -
633A SER 2.9 31.4 + - - -
634A PRO* 3.5 25.7 + - - +
635A GLU* 4.6 2.0 - - - +
636A PRO* 5.1 4.6 - - - +
651A THR* 4.4 6.7 + - - +
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Residues in contact with GLN 610 (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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608A THR* 3.2 8.0 + - - +
609A ARG* 1.3 76.9 - - - +
611A GLU* 1.3 64.7 + - + +
613A PHE* 3.4 6.4 + - - -
614A GLN* 2.8 28.7 + - + +
629A LEU* 3.2 35.5 - - + +
630A PHE 3.3 22.6 + - - +
631A LYS* 3.8 13.0 - - - +
632A SER* 4.5 4.8 - - - +
765A GLN* 5.2 4.9 + - - +
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Residues in contact with GLU 611 (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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605A HIS* 3.0 40.7 + - - -
607A MET* 3.4 20.7 - - + +
608A THR* 3.0 41.6 + - - +
610A GLN* 1.3 78.3 - - + +
612A ILE* 1.3 60.7 + - - +
614A GLN* 3.4 7.8 + - + +
615A GLU* 3.1 18.9 + - - +
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Residues in contact with ILE 612 (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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607A MET* 3.7 33.7 - - + +
608A THR 3.0 23.1 + - - +
609A ARG* 3.7 11.0 - - - +
611A GLU* 1.3 75.1 - - - +
613A PHE* 1.3 67.5 + - + +
615A GLU* 3.2 8.5 + - - +
616A GLN* 3.0 43.1 + - + +
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Residues in contact with PHE 613 (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 ARG* 3.0 65.8 + - + +
610A GLN* 3.8 1.8 - - - +
612A ILE* 1.3 76.5 - - + +
614A GLN* 1.3 57.9 + - - +
616A GLN* 3.2 20.5 + - - +
617A LEU* 2.8 36.7 + - + +
629A LEU* 3.7 17.3 - - + -
632A SER* 3.5 16.6 - - - -
651A THR* 4.2 8.7 - - + -
653A HIS* 3.5 28.0 - + + -
662A GLN* 3.8 18.6 - - - -
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Residues in contact with GLN 614 (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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610A GLN* 2.8 19.8 + - + +
611A GLU* 3.5 9.2 - - - +
612A ILE 3.2 0.2 - - - -
613A PHE* 1.3 75.3 - - - +
615A GLU* 1.3 57.8 + - - +
617A LEU* 4.8 5.3 - - - +
618A ALA* 2.9 42.9 + - + +
627A GLY 4.9 3.4 + - - -
628A PRO* 3.5 12.9 - - - +
629A LEU* 2.8 44.9 + - + +
655A PHE* 5.0 3.2 - - - -
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Residues in contact with GLU 615 (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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607A MET* 3.6 27.8 - - + +
611A GLU 3.1 13.6 + - - +
612A ILE* 3.2 12.9 + - - +
614A GLN* 1.3 76.2 - - - +
616A GLN* 1.3 68.0 + - + +
618A ALA* 3.5 4.6 + - - +
619A ALA* 3.2 22.3 + - - +
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Residues in contact with GLN 616 (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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612A ILE* 3.0 37.0 + - + +
613A PHE* 3.6 29.0 - - - +
615A GLU* 1.3 77.2 - - + +
617A LEU* 1.3 67.2 + - + +
619A ALA* 3.3 17.7 + - - +
620A VAL* 3.7 11.5 + - - +
662A GLN* 4.7 9.2 + - - +
707A TYR* 4.9 9.9 + - - +
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Residues in contact with LEU 617 (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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613A PHE* 2.8 27.9 + - + +
614A GLN* 4.1 5.6 - - - +
616A GLN* 1.3 72.2 - - + +
618A ALA* 1.3 64.4 + - - +
620A VAL* 3.1 24.9 + - - +
623A PHE* 3.6 28.8 - - + +
629A LEU* 4.1 10.1 - - + -
653A HIS* 3.8 40.6 - - + +
655A PHE* 4.0 24.2 - - + -
660A VAL* 4.3 3.4 - - + -
662A GLN* 4.7 1.1 - - - +
707A TYR* 3.6 34.3 - - + +
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Residues in contact with ALA 618 (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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614A GLN* 2.9 31.7 + - + +
615A GLU* 4.0 5.6 - - - +
616A GLN 3.4 0.2 - - - -
617A LEU* 1.3 76.2 - - - +
619A ALA* 1.3 59.8 + - - +
620A VAL 3.6 3.2 + - - +
623A PHE 5.6 4.7 - - - -
624A ARG* 3.6 25.3 + - - +
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Residues in contact with ALA 619 (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 GLU 3.2 12.5 + - - +
616A GLN* 3.5 12.6 - - - +
617A LEU 3.1 1.2 - - - -
618A ALA* 1.3 75.6 - - - +
620A VAL* 1.3 60.7 + - - +
621A PRO* 3.4 8.5 - - - +
624A ARG* 4.6 5.8 + - - +
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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