Contacts of the helix formed by residues 674 - 678 (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 ASP 674 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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664C ARG* 4.3 0.7 + - - -
670C GLU 5.1 0.4 - - - -
671C SER 4.1 9.4 + - - +
672C LEU 2.9 11.2 + - - +
673C LEU* 1.3 70.4 - - - +
675C PRO* 1.3 74.9 - - - +
676C ALA* 2.9 30.3 + - - +
677C LEU* 3.1 22.1 + - + +
678C ASN* 4.4 1.4 + - - +
729C HIS* 5.1 0.9 + - - -
766C ILE* 5.0 0.3 - - - +
772C TYR* 2.6 41.6 + - - +
779C LYS* 5.4 2.0 - - - +
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Residues in contact with PRO 675 (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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664C ARG* 3.8 29.4 - - - +
673C LEU 3.3 5.6 - - - +
674C ASP* 1.3 90.6 - - - +
676C ALA* 1.3 60.6 + - - +
677C LEU 3.0 0.7 - - - -
678C ASN* 3.0 37.5 + - - +
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Residues in contact with ALA 676 (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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674C ASP* 2.9 23.8 + - - +
675C PRO* 1.3 79.2 - - - +
677C LEU* 1.3 59.9 + - - +
678C ASN 3.6 1.0 + - - +
679C ARG* 3.6 14.9 + - - -
763C PHE* 4.3 3.5 - - - -
764C GLU 4.6 13.9 - - - +
765C GLY* 5.8 1.6 - - - -
766C ILE* 4.6 16.4 - - + +
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Residues in contact with LEU 677 (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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672C LEU 4.3 2.0 - - - +
674C ASP* 3.4 17.5 - - + +
675C PRO 3.0 0.8 - - - -
676C ALA* 1.3 76.6 - - - +
678C ASN* 1.3 67.1 + - - +
679C ARG* 3.0 16.2 + - - +
729C HIS* 3.5 31.6 - - + +
733C TYR* 3.3 34.7 - - + -
737C LEU* 4.0 13.9 - - + -
763C PHE* 3.9 12.5 - - + -
766C ILE* 3.7 27.1 - - + -
772C TYR* 3.6 29.8 - - + +
776C TYR* 4.7 4.7 - - + -
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Residues in contact with ASN 678 (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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657C GLU* 3.3 31.3 - - - +
660C VAL* 5.4 3.5 - - - +
661C ASP* 5.1 9.2 + - - +
664C ARG* 4.7 6.9 + - - +
674C ASP 5.0 0.7 - - - +
675C PRO* 3.0 34.7 + - - +
676C ALA 3.3 1.2 - - - +
677C LEU* 1.3 75.2 - - - +
679C ARG* 1.3 76.5 + - - +
680C ALA 4.9 0.4 - - - +
681C GLU 5.5 1.1 - - - +
682C VAL* 4.4 6.6 - - - +
733C TYR* 4.4 1.8 + - - -
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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