Contacts of the helix formed by residues 694 - 701 (chain C) in PDB entry 1DQ8
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 ALA 694 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689C THR* 3.5 36.1 - - + +
692C LYS 3.4 2.4 + - - +
693C PRO* 1.3 75.8 - - - +
695C ALA* 1.3 64.5 + - - +
696C ILE* 3.3 5.5 + - + -
697C ASN* 3.3 16.2 + - - +
698C TRP* 3.7 8.0 + - - +
746C ILE* 4.8 4.6 - - - +
776C ASN* 4.9 4.4 + - - +
743D ALA* 3.5 16.6 - - + +
744D GLY 3.7 6.3 - - - -
745D SER* 4.1 2.7 - - - +
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Residues in contact with ALA 695 (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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744A GLY* 5.4 0.2 - - - -
695B ALA* 3.5 31.9 - - + -
699B ILE* 3.8 9.0 - - + -
746B ILE* 5.7 0.4 - - + -
694C ALA* 1.3 73.0 - - - +
696C ILE* 1.3 58.3 + - - +
698C TRP* 3.0 4.6 + - - +
699C ILE* 2.8 33.5 + - + +
746C ILE* 3.9 24.3 - - + +
743D ALA 3.1 1.6 + - - +
744D GLY* 2.9 20.9 + - - +
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Residues in contact with ILE 696 (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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699B ILE* 3.4 26.6 - - + +
635C HIS* 4.2 0.7 - - - +
646C ARG* 3.6 32.5 - - - +
687C TYR* 3.6 39.3 - - + +
689C THR* 3.5 24.7 - - - +
694C ALA* 4.1 2.2 - - + -
695C ALA* 1.3 76.6 - - - +
697C ASN* 1.3 67.7 + - - +
699C ILE* 4.6 1.8 - - - +
700C GLU* 2.8 47.9 + - - +
743D ALA* 3.0 22.1 + - + +
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Residues in contact with ASN 697 (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 ARG* 3.1 13.9 + - - -
689C THR* 2.7 53.0 + - - +
692C LYS 4.6 7.1 + - - -
694C ALA 3.3 9.4 + - - +
695C ALA 3.2 0.6 - - - -
696C ILE* 1.3 79.3 - - - +
698C TRP* 1.3 58.2 + - - +
701C GLY* 2.9 33.8 + - - -
702C ARG* 3.7 13.8 - - - +
773C GLY* 5.0 8.9 - - - -
776C ASN* 4.3 6.7 - - - +
798C PRO* 4.3 1.0 - - - +
799C SER* 3.8 20.5 - - - -
801C GLU* 4.3 5.1 + - - -
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Residues in contact with TRP 698 (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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741A ALA 2.9 22.0 + - - -
742A MET* 3.6 47.0 + - + +
744A GLY* 4.5 8.5 - - - -
637B SER* 5.7 0.7 + - - -
694C ALA 3.7 3.6 + - - +
695C ALA* 3.0 14.5 + - - +
697C ASN* 1.3 82.5 - - - +
699C ILE* 1.3 66.3 + - + +
746C ILE* 4.5 7.6 - - + -
747C GLY* 3.6 32.3 - - - +
749C TYR* 4.2 12.3 - + - -
776C ASN* 3.8 14.7 - - + +
777C CYS* 3.8 18.8 - - - -
778C ILE* 3.9 29.2 - - + -
798C PRO* 3.5 51.3 - - + +
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Residues in contact with ILE 699 (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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742A MET 3.9 18.4 - - - +
743A ALA 3.7 9.9 - - - +
744A GLY* 4.6 0.7 - - - +
635B HIS* 3.1 24.5 + - - +
637B SER* 5.3 3.3 - - - -
687B TYR* 4.3 6.2 + - - +
695B ALA* 3.8 14.8 - - + +
696B ILE* 3.5 57.0 - - + +
699B ILE* 4.3 7.0 - - + -
700B GLU* 4.2 3.4 - - - +
695C ALA* 2.8 21.8 + - + +
696C ILE* 4.2 3.1 - - - +
698C TRP* 1.3 86.4 - - + +
700C GLU* 1.3 72.4 + - - +
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Residues in contact with GLU 700 (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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635B HIS* 3.1 23.9 - - + -
699B ILE* 3.9 6.1 - - - +
700B GLU* 2.7 31.7 - - - +
633C LYS* 4.6 17.5 - - - +
635C HIS* 3.4 31.4 + - + -
646C ARG* 3.4 25.0 + - - +
648C GLN* 4.8 7.5 + - - +
696C ILE* 2.8 25.8 + - + +
699C ILE* 1.3 79.2 - - - +
701C GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 701 (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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585C ALA* 6.3 0.2 - - - -
646C ARG* 2.9 26.7 + - - -
648C GLN* 4.5 5.0 + - - -
697C ASN 2.9 20.3 + - - +
698C TRP 4.4 0.8 + - - -
699C ILE 3.6 1.6 - - - -
700C GLU* 1.3 82.9 - - - +
702C ARG* 1.3 59.4 + - - -
705C SER* 4.0 8.1 - - - -
798C PRO* 3.2 18.6 - - - +
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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