Contacts of the helix formed by residues 648 - 661 (chain A) in PDB entry 5IJ7
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 GLN 648 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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647A SER* 1.3 72.9 - - - +
649A ASP* 1.3 59.2 + - - +
651A ALA* 3.3 7.4 + - - +
652A ASP* 3.0 40.6 + - - +
668A ASN* 3.3 20.3 + - - +
670A ASN 3.5 12.6 - - - +
671A ASN* 3.4 27.6 - - - +
672A ASP* 3.6 10.4 + - - +
673A PHE 4.1 1.0 - - - +
674A VAL* 3.7 20.6 - - - +
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Residues in contact with ASP 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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124A ASP* 3.9 15.7 - - - +
647A SER* 3.7 2.0 + - - +
648A GLN* 1.3 76.0 - - - +
650A GLU* 1.4 60.7 + - - +
652A ASP* 3.1 12.9 + - - +
653A ARG* 2.9 41.7 + - - +
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Residues in contact with GLU 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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122A VAL* 5.2 4.0 - - + +
123A GLU 5.3 0.7 - - - -
124A ASP* 3.0 36.0 - - - +
646A ILE* 3.9 21.5 - - + -
647A SER* 3.1 20.7 + - - +
649A ASP* 1.4 75.6 - - - +
651A ALA* 1.3 58.7 + - - +
653A ARG* 3.1 32.9 + - - +
654A ARG* 2.8 67.8 + - - +
679A ARG* 5.5 0.5 + - - -
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Residues in contact with ALA 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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646A ILE* 3.7 19.9 - - + +
647A SER 3.0 13.1 + - - +
648A GLN* 3.5 10.8 - - - +
649A ASP 3.2 0.2 - - - -
650A GLU* 1.3 76.8 - - - +
652A ASP* 1.4 53.9 + - - +
654A ARG* 3.8 1.1 - - - +
655A GLY* 2.8 32.4 + - - -
666A LEU* 3.9 16.8 - - + +
674A VAL* 3.9 22.4 - - + -
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Residues in contact with ASP 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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648A GLN* 3.0 30.0 + - - +
649A ASP* 3.1 13.1 + - - +
651A ALA* 1.4 75.3 - - - +
653A ARG* 1.3 66.6 + - - +
655A GLY* 3.5 6.5 + - - -
656A LYS* 3.5 23.1 + - - +
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Residues in contact with ARG 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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124A ASP* 3.6 32.3 + - - +
649A ASP* 2.9 22.4 + - - +
650A GLU* 3.1 44.6 + - - +
652A ASP* 1.3 75.5 - - - +
654A ARG* 1.4 62.0 + - + +
656A LYS* 3.2 31.7 + - + +
657A VAL* 4.1 5.9 + - - +
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Residues in contact with ARG 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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122A VAL* 3.9 11.1 - - - +
644A GLU* 2.6 30.5 + - - -
646A ILE* 3.5 25.7 - - + +
650A GLU* 2.8 49.0 + - - +
651A ALA* 3.9 5.6 - - - +
653A ARG* 1.4 71.8 - - + +
655A GLY* 1.3 62.5 + - - +
657A VAL* 3.2 11.9 + - - +
658A TYR* 3.2 39.2 + - + -
676A ASP* 2.8 36.9 + - - +
679A ARG* 3.8 39.3 - - - +
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Residues in contact with GLY 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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651A ALA 2.8 21.5 + - - -
652A ASP* 3.9 3.4 - - - -
653A ARG 3.3 0.6 - - - -
654A ARG* 1.3 70.2 - - - +
656A LYS* 1.3 63.1 + - - +
658A TYR* 3.7 13.8 - - - +
659A ASP* 3.1 32.5 + - - +
666A LEU* 5.0 4.9 - - - -
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Residues in contact with LYS 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 ASP* 3.5 18.4 + - - +
653A ARG* 3.2 19.4 + - + +
655A GLY* 1.3 75.9 - - - +
657A VAL* 1.3 61.8 + - + +
659A ASP* 3.7 9.5 + - - +
660A LYS* 3.6 21.7 + - - +
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Residues in contact with VAL 657 (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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653A ARG 4.5 7.4 - - - +
654A ARG* 3.2 12.5 + - + +
656A LYS* 1.3 74.0 - - + +
658A TYR* 1.3 68.1 + - + +
660A LYS* 3.2 40.4 + - + +
661A TYR* 3.3 15.8 - - + -
679A ARG* 6.1 0.7 - - - +
9001A 6BN 3.7 38.6 - - + +
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Residues in contact with TYR 658 (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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654A ARG* 3.2 23.4 + - + -
655A GLY* 3.3 9.8 + - - +
657A VAL* 1.3 77.0 - - + +
659A ASP* 1.3 56.9 + - - +
661A TYR* 2.9 19.9 + - - +
662A MET 3.0 9.7 + - - -
663A CYS* 3.4 33.5 + - - +
664A SER* 5.2 0.4 - - - -
665A PHE 5.2 2.9 - - - -
666A LEU* 3.8 31.0 - - + -
676A ASP* 2.7 30.3 + - - -
678A THR* 3.4 24.9 - - + -
679A ARG* 2.9 33.1 + - - -
9001A 6BN 3.6 29.8 - - + -
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Residues in contact with ASP 659 (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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655A GLY 3.1 19.2 + - - +
656A LYS* 4.0 7.1 - - - +
657A VAL 3.3 0.4 - - - -
658A TYR* 1.3 73.8 - - - +
660A LYS* 1.4 65.4 + - - +
662A MET* 3.2 38.9 + - + +
663A CYS 5.0 3.0 - - - +
664A SER* 6.0 1.4 - - - -
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Residues in contact with LYS 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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656A LYS* 3.6 16.8 - - - +
657A VAL* 3.2 34.4 + - + +
659A ASP* 1.4 76.6 - - - +
661A TYR* 1.4 67.0 + - + +
662A MET* 4.0 5.1 + - - +
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Residues in contact with TYR 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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111A TYR* 3.7 20.8 + - - -
657A VAL* 3.3 28.0 - - + -
658A TYR 2.9 7.6 + - - +
660A LYS* 1.4 86.2 - - + +
662A MET* 1.3 70.8 + - - +
663A CYS* 3.2 15.0 + - - +
9001A 6BN 3.7 78.1 - + + +
197E LYS* 5.7 4.9 - - - -
223E ASP* 5.2 0.9 + - - -
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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