Contacts of the helix formed by residues 737 - 743 (chain C) in PDB entry 1DQA
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 LEU 737 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733A ILE* 4.3 13.5 - - + -
737A LEU* 4.2 26.9 - - + -
738A VAL* 3.9 27.1 - - + +
741A ALA* 5.5 0.2 - - + -
749A TYR* 5.4 0.3 - - - -
732C ASN* 4.4 5.4 - - - +
733C ILE* 3.2 28.8 + - + +
736C ASN* 1.3 85.6 - - - +
738C VAL* 1.3 67.5 + - - +
739C GLY 3.5 0.2 - - - -
740C SER* 3.5 1.2 + - - -
741C ALA* 3.1 25.6 + - - +
749C TYR* 4.3 9.4 - - + -
778C ILE* 4.0 28.9 - - + -
779C THR 4.8 2.9 - - - +
780C LEU* 4.1 15.3 - - + -
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Residues in contact with VAL 738 (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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737A LEU* 3.9 16.8 - - + -
778A ILE* 3.9 17.9 - - + -
780A LEU* 3.8 26.5 - - + -
733C ILE* 2.9 23.3 + - + +
734C ASN* 3.7 15.0 - - - +
737C LEU* 1.3 74.3 - - - +
739C GLY* 1.3 56.8 + - - +
741C ALA* 3.2 6.7 + - - +
742C MET* 2.9 32.9 + - + +
639D ALA* 4.0 16.8 - - + -
642D ASN* 4.4 1.8 - - - +
644D TYR* 3.1 25.4 - - + +
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Residues in contact with GLY 739 (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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734C ASN 3.0 11.7 + - - -
735C LYS 3.2 3.8 + - - -
738C VAL* 1.3 75.0 - - - +
740C SER* 1.3 62.8 + - - +
742C MET* 3.2 4.2 + - - +
743C ALA* 3.0 24.1 + - - +
644D TYR* 3.5 16.8 - - - -
685D GLY 3.3 25.4 - - - -
686D ASN* 3.8 4.9 - - - +
687D TYR* 4.5 1.4 - - - -
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Residues in contact with SER 740 (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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735C LYS 3.1 4.8 + - - -
736C ASN 3.5 17.9 + - - -
737C LEU 3.5 0.6 + - - -
738C VAL 3.3 0.4 - - - -
739C GLY* 1.3 76.2 - - - +
741C ALA* 1.3 60.4 + - - +
743C ALA* 3.4 5.8 + - - -
744C GLY 3.2 3.8 + - - -
745C SER* 3.0 35.6 + - - -
748C GLY 2.8 27.1 + - - -
749C TYR* 3.7 13.9 - - - -
686D ASN* 2.8 26.4 + - - +
689D THR* 6.3 0.4 - - - -
692D LYS* 5.3 0.3 - - - +
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Residues in contact with ALA 741 (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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698A TRP* 2.8 26.7 + - + -
737A LEU* 5.6 0.2 - - + -
746A ILE* 6.0 0.3 - - - -
747A GLY 5.4 0.2 + - - -
749A TYR* 3.5 50.6 - - + -
778A ILE* 4.6 6.5 - - + -
737C LEU 3.1 18.6 + - - +
738C VAL* 3.5 7.4 - - - +
739C GLY 3.2 0.2 - - - -
740C SER* 1.3 75.6 - - - +
742C MET* 1.3 56.6 + - - +
744C GLY* 3.0 10.2 + - - -
745C SER 4.9 1.3 - - - +
749C TYR* 4.3 2.9 - - + -
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Residues in contact with MET 742 (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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698A TRP* 3.6 38.3 + - + +
699A ILE* 3.8 12.6 - - - +
778A ILE* 4.3 13.2 - - + -
796A THR* 5.6 1.3 - - + -
798A PRO* 6.6 0.2 - - + -
738C VAL* 2.9 20.7 + - + +
739C GLY* 3.5 7.9 - - - +
741C ALA* 1.3 75.4 - - - +
743C ALA* 1.3 60.0 + - - +
744C GLY 3.4 0.7 + - - -
637D SER* 3.2 25.9 + - - +
638D ILE 3.4 22.9 - - - +
639D ALA* 4.0 13.2 - - + -
644D TYR* 3.9 24.2 - - + -
687D TYR* 3.8 25.3 - - + -
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Residues in contact with ALA 743 (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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699A ILE* 3.8 4.5 - - - +
739C GLY 3.0 9.5 + - - +
740C SER* 3.7 7.4 - - - +
741C ALA 3.2 0.4 - - - -
742C MET* 1.3 75.4 - - - +
744C GLY* 1.3 60.7 + - - +
745C SER* 4.6 0.7 - - - +
686D ASN 3.5 13.7 - - - +
687D TYR* 4.1 9.6 - - + -
689D THR* 3.2 27.1 - - + +
694D ALA* 4.0 6.3 - - + -
695D ALA 3.3 1.9 + - - -
696D ILE* 3.1 35.8 + - + +
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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