Contacts of the helix formed by residues 739 - 749 (chain A) in PDB entry 3DBQ
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 ASN 739 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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737A ILE* 3.7 2.3 - - - +
738A ILE* 1.3 77.5 - - - +
740A GLN* 1.3 57.7 + - - +
741A ILE* 3.0 18.5 + - - +
742A SER* 2.8 67.2 + - - +
743A LYS 3.3 5.2 + - - -
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Residues in contact with GLN 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A GLY 5.3 2.9 - - - +
686A THR* 5.7 1.4 - - - -
687A VAL* 4.8 17.4 + - + +
738A ILE* 2.7 26.4 + - - +
739A ASN* 1.3 72.2 + - - +
741A ILE* 1.3 65.0 + - + +
742A SER 3.0 0.7 + - - -
743A LYS* 3.4 41.3 + - - +
744A LEU* 3.4 21.4 + - + +
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Residues in contact with ILE 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739A ASN* 3.0 14.3 + - - +
740A GLN* 1.3 80.0 - - + +
742A SER* 1.3 60.4 + - - +
744A LEU* 4.0 10.3 + - + +
745A HIS* 3.1 40.6 + - + +
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Residues in contact with SER 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737A ILE* 3.3 20.6 - - - -
739A ASN* 2.8 38.3 + - - +
741A ILE* 1.3 76.0 - - - +
743A LYS* 1.3 64.0 + - - -
745A HIS* 2.8 17.9 + - - +
746A ALA* 2.9 12.6 + - - +
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Residues in contact with LYS 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A THR* 4.9 3.4 - - - +
687A VAL* 5.1 4.4 - - + +
688A ASN* 3.1 47.2 + - - +
734A PHE* 3.2 18.8 - - + +
735A GLN* 4.2 7.3 + - - +
737A ILE* 2.9 39.6 - - + +
738A ILE* 5.0 1.2 - - - +
739A ASN 3.3 5.1 + - - +
740A GLN* 3.4 33.8 + - - +
742A SER* 1.3 76.0 - - - +
744A LEU* 1.3 58.5 + - + +
746A ALA* 2.8 8.2 + - - +
747A ILE* 2.7 47.8 + - + +
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Residues in contact with LEU 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A VAL* 3.1 40.6 - - + -
690A MET* 4.2 7.2 - - + -
695A ILE* 3.7 26.5 - - + +
740A GLN* 3.4 18.8 + - + +
741A ILE* 4.1 9.0 - - + +
742A SER 3.2 0.6 - - - -
743A LYS* 1.3 77.4 - - + +
745A HIS* 1.3 59.7 + - + +
747A ILE* 4.0 7.2 - - + -
748A ILE* 3.2 31.5 + - - +
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Residues in contact with HIS 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A ILE* 3.1 35.4 + - + +
742A SER* 2.8 10.9 + - - +
744A LEU* 1.3 78.7 - - + +
746A ALA* 1.3 60.5 + - - +
748A ILE* 3.4 19.5 - - + +
749A ASP* 3.0 30.9 + - - +
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Residues in contact with ALA 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734A PHE* 3.3 6.7 - - + -
737A ILE* 3.4 24.2 - - + -
742A SER 2.9 7.2 + - - +
743A LYS 2.8 6.1 + - - +
745A HIS* 1.3 76.9 - - - +
747A ILE* 1.3 61.2 + - - +
748A ILE 3.2 0.8 + - - -
749A ASP* 3.5 3.2 + - - -
752A HIS* 3.2 38.0 - - + +
774A ARG* 2.9 25.1 + - - -
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Residues in contact with ILE 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A VAL 3.6 24.2 - - - +
688A ASN* 5.2 2.2 - - - +
690A MET 3.4 21.5 - - - +
692A PRO* 3.3 31.4 - - + +
695A ILE* 4.1 8.3 - - + -
718A TRP* 3.9 9.7 - - + -
734A PHE* 3.6 29.4 - - + -
743A LYS* 2.7 36.5 + - + +
744A LEU* 4.0 19.3 - - + +
745A HIS 3.4 0.2 - - - -
746A ALA* 1.3 72.7 - - - +
748A ILE* 1.3 58.0 + - - +
774A ARG* 3.2 17.7 + - - -
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Residues in contact with ILE 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A PRO* 3.4 33.7 - - + +
695A ILE* 3.7 22.4 - - + -
696A LYS* 3.5 30.9 + - + +
744A LEU 3.2 20.6 - - - +
745A HIS* 3.4 28.3 - - + +
747A ILE* 1.3 82.7 - - - +
749A ASP* 1.3 59.6 + - - +
750A PRO* 3.1 14.9 - - - +
774A ARG* 4.3 5.4 - - - +
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Residues in contact with ASP 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745A HIS 3.0 21.0 + - - +
746A ALA* 3.5 1.4 + - - -
748A ILE* 1.3 75.6 - - - +
750A PRO* 1.3 57.7 - - - +
751A ASN* 2.8 42.2 + - - +
752A HIS* 2.8 27.9 + - + +
774A ARG* 2.6 29.3 + - - -
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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