Contacts of the helix formed by residues 668 - 681 (chain A) in PDB entry 2IUK
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 ASP 668 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.4 11.3 - - + +
177A PRO* 3.3 16.8 - - - +
548A HIS* 2.9 19.3 + - - -
659A TYR* 2.7 26.5 + - + -
664A ALA 3.3 15.2 + - - +
665A VAL 3.9 2.0 + - - +
666A GLN 3.4 1.8 - - - -
667A GLN* 1.3 72.4 - - - +
669A THR* 1.3 61.7 + - - +
670A GLU 3.0 8.5 + - - -
671A LEU* 3.0 39.1 + - + -
672A GLN* 3.1 29.4 + - - +
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Residues in contact with THR 669 (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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177A PRO* 3.9 19.6 - - + +
178A SER* 5.1 4.5 - - - +
189A LYS* 4.2 9.0 + - - -
667A GLN 3.0 13.3 + - - +
668A ASP* 1.3 72.9 + - - +
670A GLU* 1.3 68.6 + - - +
672A GLN* 4.2 5.1 - - - +
673A ALA* 3.5 19.4 + - - +
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Residues in contact with GLU 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PRO* 4.1 4.9 - - + -
188A ARG* 2.9 33.6 + - - -
189A LYS* 3.2 22.4 + - - +
192A PHE* 3.2 24.0 - - + -
543A HIS 3.2 11.8 - - - +
544A LEU* 3.2 12.0 - - - +
545A SER 3.0 23.0 + - - -
548A HIS* 3.2 16.1 - - + -
668A ASP* 3.0 8.1 + - - +
669A THR* 1.3 80.6 - - - +
671A LEU* 1.3 59.8 + - - +
672A GLN 3.3 1.1 - - - -
673A ALA* 3.6 4.3 - - - +
674A TRP* 3.1 22.0 + - - +
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Residues in contact with LEU 671 (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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544A LEU* 4.1 6.0 - - + +
548A HIS* 4.6 3.1 - - + +
550A ILE* 3.8 19.7 - - + -
659A TYR* 3.4 35.0 - - + +
665A VAL* 4.4 15.9 - - + +
668A ASP* 3.0 21.2 + - + +
670A GLU* 1.3 77.0 - - - +
672A GLN* 1.3 58.1 + - - +
674A TRP* 3.5 31.7 - - + -
675A TRP* 2.9 32.2 + - - +
695A LYS* 4.4 9.4 - - + -
701A LEU* 3.7 25.4 - - + -
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Residues in contact with GLN 672 (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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665A VAL 3.0 14.0 - - - +
666A GLN 3.8 13.4 - - - +
668A ASP 3.1 18.6 + - - +
669A THR* 4.2 6.3 - - - +
670A GLU 3.3 0.2 - - - -
671A LEU* 1.3 77.8 - - - +
673A ALA* 1.3 52.5 + - - +
675A TRP* 3.8 4.1 - - - +
676A LYS* 2.8 35.9 + - - +
695A LYS* 2.7 38.9 - - - +
696A GLN* 3.6 17.7 + - - +
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Residues in contact with ALA 673 (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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543A HIS* 3.4 29.7 + - + +
669A THR 3.5 17.0 + - - +
670A GLU* 3.6 6.3 - - - +
672A GLN* 1.3 76.9 - - - +
674A TRP* 1.4 59.5 - - - +
676A LYS* 3.7 11.5 - - - +
677A GLU* 3.0 30.1 + - - +
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Residues in contact with TRP 674 (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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536A PHE* 4.1 4.9 + + - +
539A ALA* 3.4 18.5 - - + +
540A THR* 2.8 46.0 + - - +
543A HIS* 3.5 13.7 - - + +
544A LEU* 3.3 21.0 - - + +
550A ILE* 4.6 4.7 - - + -
554A LEU* 3.7 25.1 - - + -
558A TYR* 4.6 0.9 - - - -
670A GLU 3.1 17.0 + - - +
671A LEU* 3.5 33.4 - - + +
673A ALA* 1.4 74.7 - - - +
675A TRP* 1.3 97.2 - + + +
677A GLU* 3.1 6.2 + - - +
678A ALA* 2.9 27.3 + - + +
695A LYS* 4.2 11.4 - - + -
701A LEU* 4.5 2.9 - - + -
704A SER* 5.2 2.2 - - - -
705A CYS* 4.7 7.2 - - - -
708A ILE* 4.0 19.5 - - + -
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Residues in contact with TRP 675 (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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536A PHE* 3.9 21.3 - + - -
602A PHE* 3.7 21.8 - + - -
671A LEU 2.9 18.2 + - - +
672A GLN* 4.1 3.6 - - - +
674A TRP* 1.3 99.6 - + + +
676A LYS* 1.3 65.0 + - - +
678A ALA* 3.5 11.6 + - + -
679A VAL* 3.3 35.9 - - + +
692A TRP* 4.1 12.8 - + - -
693A PRO* 2.6 45.5 + - + -
694A LYS* 4.5 4.0 - - - -
695A LYS* 3.5 33.9 - - + -
704A SER* 3.7 22.2 - - - -
708A ILE* 4.9 1.3 - - + -
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Residues in contact with LYS 676 (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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672A GLN 2.8 25.1 + - - +
673A ALA* 3.7 10.5 - - - +
674A TRP 3.3 0.2 - - - -
675A TRP* 1.3 75.3 - - - +
677A GLU* 1.3 58.7 + - + +
679A VAL* 3.9 0.8 - - - +
680A GLU* 3.0 66.8 + - - +
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Residues in contact with GLU 677 (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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212A TYR* 2.8 30.9 + - - +
539A ALA* 4.0 5.1 - - + -
542A ARG* 3.2 31.6 + - - -
543A HIS* 3.2 27.2 + - + +
673A ALA 3.0 19.8 + - - +
674A TRP 3.5 3.6 - - - +
676A LYS* 1.3 77.3 - - + +
678A ALA* 1.3 64.9 + - - +
679A VAL 3.2 2.0 - - - -
680A GLU* 4.8 0.9 - - - -
681A LYS* 2.9 39.9 + - + +
682A GLY 2.9 19.9 + - - -
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Residues in contact with ALA 678 (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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212A TYR* 4.7 0.2 - - - -
535A PRO* 4.4 4.5 - - - +
536A PHE* 3.7 32.5 - - + -
539A ALA* 4.1 15.9 - - + -
674A TRP* 2.9 16.9 + - - +
675A TRP* 4.0 17.0 - - + +
676A LYS 3.5 0.6 - - - -
677A GLU* 1.3 74.0 - - - +
679A VAL* 1.3 58.9 + - + +
682A GLY* 3.1 7.6 - - - +
683A HIS* 3.0 31.6 + - - -
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Residues in contact with VAL 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A TRP* 3.3 45.3 - - + +
676A LYS* 3.9 2.7 - - - +
678A ALA* 1.3 78.4 - - + +
680A GLU* 1.3 64.3 + - + +
683A HIS* 2.9 40.2 - - - +
684A GLY* 3.1 1.6 + - - -
687A LYS* 3.8 15.1 - - + +
692A TRP* 3.7 50.7 - - + +
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Residues in contact with GLU 680 (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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676A LYS* 3.0 59.1 + - - +
677A GLU* 4.8 0.7 - - - -
679A VAL* 1.3 87.6 - - + +
681A LYS* 1.3 66.2 + - + +
684A GLY* 3.4 12.0 - - - -
687A LYS* 3.8 46.0 - - + +
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Residues in contact with LYS 681 (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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211A ASP* 5.9 0.2 + - - -
212A TYR* 4.2 19.3 - - + -
240A LEU* 3.7 23.2 - - + +
542A ARG* 4.1 11.7 - - - +
677A GLU* 2.9 46.2 + - + +
680A GLU* 1.3 84.7 - - + +
682A GLY* 1.3 67.7 + - - +
683A HIS 3.6 0.4 - - - -
684A GLY* 3.6 7.3 + - - -
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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