Contacts of the helix formed by residues 679 - 692 (chain C) in PDB entry 1IW1
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 ARG 679 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653C TYR* 3.7 24.7 - - + -
657C GLU* 2.7 8.5 + - - -
676C ALA 3.6 11.9 + - - -
677C LEU 3.0 15.8 + - - +
678C ASN* 1.3 90.8 + - - +
680C ALA* 1.3 63.5 + - - +
681C GLU 3.3 2.2 - - - -
682C VAL* 3.2 18.5 + - - +
683C LEU* 2.8 24.9 + - + +
733C TYR* 4.1 3.8 - - + -
736C ASP* 4.3 2.9 - - - +
759C GLY 3.4 6.9 + - - -
760C PHE* 2.8 68.1 + - + +
762C HIS 3.0 25.1 + - - -
763C PHE* 3.4 33.9 - - + +
764C GLU 4.9 1.8 - - - +
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Residues in contact with ALA 680 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650C TRP* 3.3 17.0 + - + +
653C TYR* 4.5 7.1 - - - +
654C THR* 3.8 35.4 - - + +
657C GLU* 2.9 19.5 + - + +
678C ASN* 3.8 0.4 - - - +
679C ARG* 1.3 77.0 - - - +
681C GLU* 1.3 69.8 + - + +
683C LEU* 3.3 3.0 + - - +
684C ALA 3.1 17.8 + - - -
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Residues in contact with GLU 681 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B GLU* 2.6 46.5 - - + +
650C TRP* 5.9 1.3 - - - -
678C ASN* 5.5 1.4 - - - +
680C ALA* 1.3 83.1 - - + +
682C VAL* 1.3 67.1 + - + +
684C ALA* 3.3 13.8 + - - +
685C ARG* 3.1 45.6 + - - +
697C ARG* 5.8 0.2 + - - -
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Residues in contact with VAL 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678C ASN 4.4 6.5 + - - +
679C ARG* 3.2 30.1 + - - +
681C GLU* 1.3 78.8 - - + +
683C LEU* 1.3 60.6 + - - +
685C ARG* 3.2 29.8 + - - +
686C ASP* 3.0 20.7 + - - +
759C GLY* 3.2 40.8 - - - +
760C PHE* 3.3 9.0 - - - +
762C HIS 5.7 0.4 - - - +
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Residues in contact with LEU 683 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646C GLN* 3.7 42.0 - - + +
649C ALA* 3.7 9.6 - - + +
650C TRP* 3.7 35.2 - - + +
653C TYR* 3.9 16.6 - - + -
679C ARG 2.8 16.8 + - - +
680C ALA* 3.5 4.7 - - - +
682C VAL* 1.3 78.5 - - - +
684C ALA* 1.3 56.5 + - - +
686C ASP* 3.1 9.6 + - + +
687C LEU* 2.9 33.1 + - - +
760C PHE* 3.4 37.2 - - + -
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Residues in contact with ALA 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650C TRP* 3.7 23.7 - - + +
680C ALA 3.1 8.0 + - - +
681C GLU* 3.7 19.1 - - - +
682C VAL 3.3 0.2 - - - -
683C LEU* 1.3 76.0 - - - +
685C ARG* 1.3 58.1 + - + +
687C LEU* 3.3 2.8 + - - +
688C ASP* 3.0 34.7 + - - +
696C TRP* 3.8 10.7 - - + -
697C ARG* 3.6 21.3 - - - +
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Residues in contact with ARG 685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681C GLU* 3.1 31.3 + - - +
682C VAL* 3.3 38.6 - - + +
683C LEU 3.2 0.2 - - - -
684C ALA* 1.3 75.2 - - + +
686C ASP* 1.3 64.4 + - - +
688C ASP* 3.2 13.9 + - - +
689C LYS* 3.1 43.5 + - - +
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Residues in contact with ASP 686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646C GLN* 4.8 4.0 - - + +
682C VAL* 3.0 15.1 + - - +
683C LEU* 3.4 13.2 - - + +
685C ARG* 1.3 75.7 - - - +
687C LEU* 1.3 52.5 + - + +
689C LYS* 3.1 5.8 + - - +
690C LEU* 2.7 44.4 + - + +
756C GLU 3.5 7.2 - - - +
757C ALA* 3.3 27.9 - - - +
758C LEU* 3.7 0.7 - - - -
759C GLY* 2.8 23.2 + - - -
760C PHE* 2.8 35.9 + - - +
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Residues in contact with LEU 687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643C THR* 3.9 9.9 - - + +
646C GLN* 3.8 37.9 - - + +
647C GLU* 3.6 30.1 - - + -
650C TRP* 4.0 9.4 - - + -
683C LEU 2.9 19.3 + - - +
684C ALA 3.6 1.3 - - - +
686C ASP* 1.3 74.0 - - + +
688C ASP* 1.3 61.4 + - - +
690C LEU* 4.2 4.9 - - + +
691C ASN* 2.8 46.9 + - - +
696C TRP* 3.5 44.4 - - + -
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Residues in contact with ASP 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B GLN* 2.8 33.9 - - - +
417B ARG* 5.4 2.8 + - - +
684C ALA 3.0 18.1 + - - +
685C ARG* 3.4 18.0 - - - +
687C LEU* 1.3 76.0 - - - +
689C LYS* 1.3 59.8 + - + +
692C GLY* 3.1 22.0 + - - -
693C SER* 3.1 17.7 + - - +
694C SER* 3.6 4.5 - - - -
696C TRP* 2.9 8.7 + - - -
697C ARG* 2.8 30.9 + - - -
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Residues in contact with LYS 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685C ARG* 3.1 37.4 + - - +
686C ASP* 3.5 7.1 + - - +
688C ASP* 1.3 77.2 - - + +
690C LEU* 1.3 65.3 + - - +
692C GLY* 3.2 11.5 + - - -
756C GLU* 2.9 65.0 + - + +
757C ALA* 4.1 10.5 - - + -
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Residues in contact with LEU 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639C VAL* 4.2 23.6 - - + +
642C PHE* 3.9 24.5 - - + -
643C THR* 3.9 22.5 + - + +
646C GLN* 4.5 8.7 - - + -
686C ASP* 2.7 30.1 + - + +
687C LEU* 4.0 16.6 - - + +
689C LYS* 1.3 73.8 - - - +
691C ASN* 1.3 61.4 + - - +
692C GLY 3.6 0.2 + - - -
753C VAL* 3.9 18.4 - - + -
757C ALA* 3.6 25.4 - - + +
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Residues in contact with ASN 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643C THR* 3.7 28.2 - - - +
647C GLU* 3.8 6.8 + - - +
687C LEU* 2.8 30.3 + - - +
690C LEU* 1.3 77.8 - - - +
692C GLY* 1.3 61.3 + - - +
693C SER* 3.3 9.1 + - - +
696C TRP* 3.6 40.0 - - + +
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Residues in contact with GLY 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B GLU* 4.5 0.9 - - - +
417B ARG* 4.0 12.5 + - - -
418B ASP* 5.6 0.7 - - - +
688C ASP 3.1 11.7 + - - -
689C LYS* 3.2 11.3 + - - -
690C LEU 3.3 0.4 + - - -
691C ASN* 1.3 73.7 - - - +
693C SER* 1.3 64.0 + - - +
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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