Contacts of the helix formed by residues 626 - 634 (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 SER 626 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622C LYS 3.0 14.0 + - - -
623C ALA* 3.5 10.2 + - - -
624C GLU 3.5 1.0 + - - -
625C HIS* 1.3 76.8 - - - +
627C THR* 1.3 53.7 + - - +
628C PHE* 3.8 2.2 + - - -
629C MET* 3.3 26.9 + - - +
630C SER* 2.7 36.4 + - - -
805C HIS* 4.9 13.5 - - - -
808C PHE* 3.9 21.1 - - - +
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Residues in contact with THR 627 (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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625C HIS 3.6 2.0 + - - -
626C SER* 1.3 73.4 - - - +
628C PHE* 1.3 63.5 + - - +
630C SER* 2.9 17.4 + - - +
631C ASP* 3.0 37.2 + - - +
812C GLY* 6.3 2.7 - - - -
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Residues in contact with PHE 628 (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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626C SER* 3.2 5.0 - - - +
627C THR* 1.3 80.3 - - - +
629C MET* 1.3 62.6 + - - +
631C ASP* 3.4 2.2 + - - -
632C LEU* 2.8 49.6 + - + +
637C LEU* 3.7 21.8 - - + +
641C GLU* 3.7 36.3 - - + -
644C ARG* 4.6 2.7 - - - -
645C LEU* 4.2 7.4 - - + -
808C PHE* 3.6 37.7 - + - +
811C LEU* 3.7 52.5 - - + -
812C GLY* 3.9 10.0 - - - +
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Residues in contact with MET 629 (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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623C ALA 4.4 11.7 - - - +
624C GLU 4.5 2.9 - - - +
626C SER* 3.3 13.8 + - - +
628C PHE* 1.3 76.9 - - - +
630C SER* 1.3 67.3 + - - +
632C LEU* 4.0 21.3 - - + -
633C LEU* 2.8 61.1 + - + +
645C LEU* 4.1 8.3 - - - -
743C ILE* 4.2 15.3 - - + -
808C PHE* 3.3 43.3 - - + -
903C HEM 3.8 26.0 - - + -
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Residues in contact with SER 630 (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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624C GLU 4.7 4.6 + - - -
625C HIS* 4.3 15.3 + - - -
626C SER 2.7 25.0 + - - -
627C THR* 2.9 18.2 + - - +
629C MET* 1.3 78.8 - - - +
631C ASP* 1.3 66.2 + - - +
633C LEU* 3.5 4.4 + - - +
634C LYS* 3.0 25.7 + - - +
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Residues in contact with ASP 631 (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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627C THR* 3.0 43.8 + - - +
628C PHE* 3.8 3.5 - - - +
630C SER* 1.3 77.8 + - - +
632C LEU* 1.3 67.3 + - - +
634C LYS* 3.3 5.3 + - - +
635C GLY 3.2 4.2 + - - -
636C ARG* 3.1 43.6 + - + +
637C LEU* 3.8 22.3 + - + +
751C TYR* 3.7 0.2 + - - -
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Residues in contact with LEU 632 (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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628C PHE* 2.8 38.3 + - + +
629C MET* 3.2 23.5 + - + +
631C ASP* 1.3 76.7 - - - +
633C LEU* 1.3 62.2 + - - +
635C GLY 3.4 1.2 + - - -
637C LEU* 3.7 20.1 - - + +
638C GLY 4.1 3.6 - - - +
641C GLU* 4.2 0.9 - - + -
642C PHE* 4.0 26.2 - - + +
645C LEU* 4.2 12.3 - - + -
743C ILE* 5.5 1.6 - - + -
747C MET* 3.7 22.2 - - + +
750C HIS* 4.8 0.3 - - - -
751C TYR* 2.7 51.2 + - + -
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Residues in contact with LEU 633 (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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624C GLU 5.4 3.1 - - - +
629C MET* 2.8 46.4 + - + +
630C SER* 4.1 3.8 - - - +
632C LEU* 1.3 73.6 - - + +
634C LYS* 1.3 57.3 + - - +
635C GLY 3.3 0.2 - - - -
742C VAL* 5.2 2.2 - - + -
743C ILE* 3.9 21.3 - - + -
746C MET* 3.8 31.2 - - + +
747C MET* 4.0 11.2 - - + -
750C HIS* 3.0 24.7 + - - -
903C HEM 3.8 34.5 - - + -
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Residues in contact with LYS 634 (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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630C SER 3.0 19.1 + - - +
631C ASP* 3.8 7.4 - - - +
632C LEU 3.3 0.4 - - - -
633C LEU* 1.3 77.3 - - - +
635C GLY* 1.3 58.7 + - - +
636C ARG* 4.4 18.8 - - + +
750C HIS* 3.3 16.6 + - - -
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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