Contacts of the helix formed by residues 648 - 661 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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647B SER* 1.3 72.5 - - - +
649B ASP* 1.4 59.6 + - - +
651B ALA* 3.3 7.3 + - - +
652B ASP* 3.0 42.7 + - - +
668B ASN* 3.3 20.3 + - - +
670B ASN 3.5 12.0 - - - +
671B ASN* 3.3 28.6 - - - +
672B ASP* 3.5 11.2 + - - +
673B PHE 4.1 0.9 - - - +
674B VAL* 3.7 20.1 - - - +
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Residues in contact with ASP 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ASP* 3.9 14.6 - - - +
647B SER* 3.3 2.6 + - - +
648B GLN* 1.4 76.4 - - - +
650B GLU* 1.4 60.0 + - - +
652B ASP* 3.1 13.2 + - - +
653B ARG* 2.9 41.5 + - - +
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Residues in contact with GLU 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B VAL* 5.2 3.8 - - + +
123B GLU 5.3 0.9 - - - -
124B ASP* 3.0 33.9 - - - +
646B ILE* 3.9 21.1 - - + -
647B SER* 3.1 21.1 + - - +
649B ASP* 1.4 77.3 - - - +
651B ALA* 1.3 57.5 + - - +
653B ARG* 3.1 32.2 + - - +
654B ARG* 2.8 68.5 + - - +
679B ARG* 5.5 0.5 + - - -
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Residues in contact with ALA 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646B ILE* 3.7 19.4 - - + +
647B SER 3.0 14.0 + - - +
648B GLN* 3.5 10.8 - - - +
650B GLU* 1.3 77.4 - - - +
652B ASP* 1.4 53.3 + - - +
654B ARG* 3.9 1.0 - - - +
655B GLY* 2.8 32.4 + - - -
666B LEU* 3.9 16.7 - - + +
674B VAL* 3.9 22.0 - - + -
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Residues in contact with ASP 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648B GLN* 3.0 29.9 + - - +
649B ASP* 3.1 13.7 + - - +
651B ALA* 1.4 74.2 - - - +
653B ARG* 1.3 65.5 + - - +
655B GLY* 3.5 2.3 + - - -
656B LYS* 3.5 28.3 + - - +
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Residues in contact with ARG 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 3.6 31.9 + - - +
649B ASP* 2.9 23.2 + - - +
650B GLU* 3.1 44.1 + - - +
652B ASP* 1.3 74.3 - - - +
654B ARG* 1.4 62.4 + - + +
656B LYS* 3.2 31.1 + - + +
657B VAL* 4.1 6.1 + - - +
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Residues in contact with ARG 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B VAL* 3.9 11.3 - - - +
644B GLU* 2.6 29.5 + - - -
646B ILE* 3.5 25.2 - - - +
650B GLU* 2.8 49.3 + - - +
651B ALA* 3.9 5.2 - - - +
653B ARG* 1.4 71.3 - - + +
655B GLY* 1.3 62.2 + - - +
657B VAL* 3.2 12.3 + - + +
658B TYR* 3.2 38.3 + - + -
666B LEU* 4.8 0.9 - - + -
676B ASP* 2.8 36.9 + - - +
679B ARG* 3.8 40.7 - - - +
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Residues in contact with GLY 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B ALA 2.8 20.8 + - - -
652B ASP* 3.9 3.1 - - - -
653B ARG 3.3 0.6 - - - -
654B ARG* 1.3 69.9 - - - +
656B LYS* 1.3 63.8 + - - +
658B TYR* 3.7 13.1 - - - +
659B ASP* 3.1 31.4 + - - +
666B LEU* 5.0 5.2 - - - -
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Residues in contact with LYS 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652B ASP* 3.5 22.3 + - - +
653B ARG* 3.2 17.1 + - + +
655B GLY* 1.3 76.2 - - - +
657B VAL* 1.4 62.3 + - + +
659B ASP* 3.7 10.2 + - - +
660B LYS* 3.6 20.9 + - - +
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Residues in contact with VAL 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653B ARG 4.5 7.6 - - - +
654B ARG* 3.2 12.7 + - - +
656B LYS* 1.4 72.5 - - + +
658B TYR* 1.3 66.0 + - + +
660B LYS* 3.2 40.7 + - + +
661B TYR* 3.3 15.9 - - + -
679B ARG* 6.1 0.4 - - - +
9001B 6BN 3.6 39.5 - - + +
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Residues in contact with TYR 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654B ARG* 3.2 21.3 + - + -
655B GLY* 3.3 10.3 + - - +
657B VAL* 1.3 78.5 - - + +
659B ASP* 1.3 56.6 + - - +
661B TYR* 2.9 19.3 + - - +
662B MET 3.0 10.0 + - - -
663B CYS* 3.3 34.5 + - - +
664B SER* 5.2 0.2 - - - -
665B PHE 5.2 3.6 - - - -
666B LEU* 3.8 31.4 - - + -
676B ASP* 2.7 30.3 + - - -
678B THR* 3.3 23.6 - - + -
679B ARG* 2.9 29.2 + - - -
9001B 6BN 3.6 34.8 - - + -
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Residues in contact with ASP 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655B GLY 3.1 19.2 + - - +
656B LYS* 4.0 7.3 - - - +
657B VAL 3.3 0.4 - - - -
658B TYR* 1.3 72.9 - - - +
660B LYS* 1.4 65.0 + - - +
662B MET* 3.2 39.8 + - + +
663B CYS 5.1 2.9 - - - +
664B SER* 6.0 1.9 - - - -
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Residues in contact with LYS 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656B LYS* 3.6 15.7 - - - +
657B VAL* 3.2 34.3 - - + +
659B ASP* 1.4 76.1 - - - +
661B TYR* 1.4 67.6 + - + +
662B MET* 4.9 5.7 - - - +
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Residues in contact with TYR 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B TYR* 3.7 20.5 + - - -
657B VAL* 3.3 27.6 - - + -
658B TYR 2.9 7.8 + - - +
660B LYS* 1.4 87.2 - - + +
662B MET* 1.3 71.1 + - - +
663B CYS* 3.2 15.6 + - - -
9001B 6BN 3.7 76.8 - + + +
197F LYS* 5.6 5.0 - - - -
223F ASP* 5.4 0.5 + - - -
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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