Contacts of the helix formed by residues 737 - 743 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733B ILE* 4.4 7.0 - - + -
737B LEU* 4.2 28.9 - - + -
738B VAL* 4.1 24.9 - - + +
741B ALA* 5.6 0.4 - - + -
749B TYR* 5.5 0.7 - - - -
732D ASN* 3.5 6.3 + - - +
733D ILE* 3.2 34.6 + - + +
736D ASN* 1.3 84.1 - - - +
738D VAL* 1.3 68.1 + - - +
740D SER* 3.5 1.6 + - - -
741D ALA* 3.0 24.9 + - - +
749D TYR* 4.4 9.5 - - + -
778D ILE* 3.9 29.8 - - + -
779D THR 4.8 1.8 - - - +
780D LEU* 4.1 16.8 - - + -
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Residues in contact with VAL 738 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737B LEU* 3.9 23.8 - - + -
778B ILE* 4.0 12.8 - - + -
780B LEU* 3.9 15.9 - - + -
639C ALA* 3.9 25.1 - - + -
642C ASN* 4.2 3.8 - - - +
644C TYR* 3.2 20.6 - - + +
733D ILE* 2.9 19.8 + - + +
734D ASN* 3.7 15.9 - - - +
737D LEU* 1.3 71.4 - - - +
739D GLY* 1.3 57.2 + - - +
741D ALA* 3.1 7.1 + - - +
742D MET* 2.9 33.8 + - + +
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Residues in contact with GLY 739 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644C TYR* 3.5 16.6 - - - -
685C GLY 3.3 20.2 - - - -
686C ASN* 4.0 4.7 - - - +
687C TYR* 4.6 1.0 - - - -
734D ASN 3.0 11.9 + - - -
735D LYS 3.2 9.9 + - - -
738D VAL* 1.3 74.2 - - - +
740D SER* 1.3 63.7 + - - +
742D MET* 3.1 5.0 + - - +
743D ALA* 3.0 22.7 + - - +
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Residues in contact with SER 740 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686C ASN* 3.0 23.3 + - - +
689C THR* 5.9 1.4 - - - +
692C LYS* 5.3 0.3 - - - -
735D LYS 3.1 5.3 + - - -
736D ASN 3.5 17.6 + - - -
737D LEU 3.5 0.2 + - - -
738D VAL 3.4 0.6 - - - -
739D GLY* 1.3 74.7 - - - +
741D ALA* 1.3 61.7 + - - +
743D ALA* 3.4 5.4 + - - +
744D GLY 3.3 3.8 + - - -
745D SER* 3.0 33.7 + - - -
748D GLY 2.8 27.0 + - - -
749D TYR* 3.7 13.2 - - - -
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Residues in contact with ALA 741 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698B TRP* 2.9 20.8 + - + -
737B LEU* 5.7 0.4 - - + -
746B ILE* 6.1 0.2 - - - -
747B GLY 5.5 0.3 + - - -
749B TYR* 3.6 51.2 - - + -
778B ILE* 4.5 8.3 - - + -
737D LEU 3.0 19.1 + - - +
738D VAL* 3.1 7.8 + - - +
740D SER* 1.3 77.4 - - - +
742D MET* 1.3 60.4 + - - +
744D GLY* 3.1 10.0 + - - -
745D SER 4.9 1.3 - - - +
749D TYR* 4.3 1.9 - - + -
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Residues in contact with MET 742 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698B TRP* 3.5 34.6 + - + +
699B ILE* 3.8 8.8 - - - +
778B ILE* 4.5 10.3 - - + -
796B THR* 5.8 0.2 - - + -
637C SER* 4.0 21.1 - - - +
638C ILE 3.3 31.6 - - - +
639C ALA* 4.0 12.8 - - + -
644C TYR* 3.9 23.8 - - + -
687C TYR* 3.7 24.4 - - + -
738D VAL* 2.9 23.4 + - + +
739D GLY* 3.1 7.8 + - - +
741D ALA* 1.3 75.1 - - - +
743D ALA* 1.3 59.7 + - - +
744D GLY 3.4 0.7 + - - -
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Residues in contact with ALA 743 (chain D).
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* 3.7 4.6 - - - +
686C ASN 3.6 13.0 - - - +
687C TYR* 4.0 10.1 - - + -
689C THR* 3.3 27.1 - - + +
694C ALA* 3.7 6.0 - - + +
695C ALA 3.2 2.8 + - - -
696C ILE* 3.0 36.9 + - + -
739D GLY 3.0 9.7 + - - +
740D SER* 3.8 7.2 - - - +
741D ALA 3.2 0.6 - - - -
742D MET* 1.3 76.0 - - - +
744D GLY* 1.3 60.6 + - - +
745D SER* 5.2 0.4 - - - -
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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