Contacts of the helix formed by residues 743 - 755 (chain A) in PDB entry 3E0D
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 TYR 743 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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688A GLU 4.5 0.5 + - - -
691A ILE* 3.4 13.2 - - + +
692A ALA* 2.7 38.9 + - + +
695A SER* 2.7 39.9 - - - -
736A GLU* 4.3 20.1 + - + -
737A THR* 4.9 8.5 - - - -
742A VAL* 1.3 78.5 + - + +
744A GLN* 1.3 63.0 + - - +
745A GLU* 3.8 7.6 - - + +
746A GLN* 3.0 51.1 + - + +
747A ILE* 3.4 10.6 + - - +
812A GLY* 4.6 2.0 - - - -
813A PHE* 2.3 33.7 - + + +
815A LYS* 4.6 21.3 - - + +
818A ALA* 4.9 0.9 - - + -
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Residues in contact with GLN 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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452A ARG* 2.7 36.0 + - - +
743A TYR* 1.3 66.8 - - - +
745A GLU* 1.3 62.5 + - - +
747A ILE* 3.0 14.8 + - + +
748A MET* 3.0 25.6 + - - +
766A ARG* 3.6 32.0 - - - +
809A ALA 6.0 0.7 - - - +
812A GLY* 3.2 23.1 + - - +
813A PHE* 1.8 40.1 + - - +
814A ASN* 3.6 14.1 + - - +
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Residues in contact with GLU 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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447A GLY 5.7 2.9 - - - +
448A LEU* 6.3 0.2 - - - -
449A LEU* 4.5 24.9 - - + +
452A ARG* 3.6 20.9 - - + -
743A TYR* 4.5 4.0 - - + -
744A GLN* 1.3 74.6 - - - +
746A GLN* 1.3 61.6 + - + +
748A MET* 3.4 10.1 + - - +
749A GLN* 3.0 33.6 + - - +
813A PHE 1.8 35.6 - - - +
814A ASN* 2.0 43.7 + - - +
815A LYS* 2.4 22.9 + - + -
816A SER 3.7 1.4 + - - -
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Residues in contact with GLN 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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733A ILE* 3.2 35.4 - - + +
734A LEU* 3.6 12.3 - - + +
736A GLU* 5.0 2.5 - - - +
737A THR* 2.9 26.3 - - - +
740A ILE 3.4 6.3 + - - -
741A PRO* 4.8 2.9 - - + -
742A VAL* 2.8 34.2 - - - +
743A TYR* 3.0 39.2 + - + +
745A GLU* 1.3 78.1 - - + +
747A ILE* 1.3 61.3 + - - +
749A GLN* 3.5 5.1 + - - +
750A ILE* 3.1 29.9 + - - +
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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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741A PRO* 4.5 15.0 - - + +
743A TYR 3.4 12.1 + - - +
744A GLN* 3.0 13.8 + - + +
746A GLN* 1.3 73.2 - - - +
748A MET* 1.3 67.9 + - - +
750A ILE* 3.0 9.3 + - + +
751A ALA* 2.9 24.2 + - + +
762A ALA 5.9 1.1 - - - +
765A LEU* 6.0 3.1 - - + -
766A ARG* 5.3 14.6 - - + +
769A MET* 5.5 3.8 - - - -
805A LEU* 4.2 34.7 - - + +
808A PHE* 3.8 15.0 - - + +
809A ALA* 3.7 37.9 - - + +
812A GLY* 4.7 5.4 - - - -
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Residues in contact with MET 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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449A LEU* 5.8 4.3 - - + -
451A GLU 4.8 2.0 - - - +
452A ARG* 3.6 42.8 - - + +
744A GLN 3.0 16.8 + - - +
745A GLU* 3.6 10.5 - - - +
747A ILE* 1.3 77.1 - - - +
749A GLN* 1.3 57.8 + - + +
751A ALA* 4.8 0.7 - - - -
752A SER* 2.8 30.7 + - - -
759A LEU* 3.3 37.2 - - + +
762A ALA* 3.2 30.1 - - + +
763A ASP* 3.8 24.2 - - + +
766A ARG* 4.0 14.6 - - + +
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Residues in contact with GLN 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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447A GLY 5.7 0.6 + - - -
449A LEU* 3.9 34.7 - - + +
733A ILE* 3.7 33.1 - - + +
745A GLU* 3.0 26.1 + - - +
746A GLN* 3.8 3.8 - - - +
748A MET* 1.3 73.7 - - - +
750A ILE* 1.3 60.1 + - - +
752A SER* 3.1 1.3 + - - -
753A GLN* 2.8 45.4 + - - +
759A LEU* 4.1 15.7 - - + +
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Residues in contact with ILE 750 (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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729A TYR* 6.1 1.1 - - - -
730A LEU* 3.8 33.0 - - + -
733A ILE* 3.7 19.9 - - + +
734A LEU* 3.8 27.1 - - + -
741A PRO* 5.2 2.7 - - + -
746A GLN 3.1 20.2 + - - +
747A ILE* 3.0 8.8 + - - +
749A GLN* 1.3 75.2 - - - +
751A ALA* 1.3 58.5 + - - +
753A GLN* 5.0 0.4 - - - -
754A VAL* 2.9 39.6 + - + +
784A PHE* 5.5 0.2 - - + -
801A LEU* 4.6 9.6 - - + -
804A MET* 4.3 6.3 - - + -
805A LEU* 3.8 31.9 - - + -
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Residues in contact with ALA 751 (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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747A ILE* 2.9 15.7 + - + +
748A MET* 3.8 3.8 - - - +
750A ILE* 1.3 78.5 - - - +
752A SER* 1.3 58.6 + - - +
755A ALA* 3.2 26.5 + - - +
757A TYR* 3.3 11.7 - - + +
762A ALA* 4.3 6.1 - - + +
765A LEU* 3.7 29.6 - - + -
784A PHE* 4.1 13.7 - - + -
805A LEU* 4.1 11.0 - - + -
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Residues in contact with SER 752 (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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748A MET 2.8 18.8 + - - -
749A GLN* 3.6 3.1 - - - -
751A ALA* 1.3 78.0 - - - +
753A GLN* 1.3 62.7 + - - +
756A GLY* 3.4 14.9 + - - -
757A TYR* 2.7 36.1 + - - +
759A LEU* 3.4 35.4 + - - +
762A ALA* 4.4 1.6 - - - -
791A ARG* 5.5 0.5 + - - -
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Residues in contact with GLN 753 (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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729A TYR* 3.7 36.2 + - + +
732A PRO* 6.0 3.3 - - - +
733A ILE* 3.5 29.8 - - - +
749A GLN* 2.8 25.8 + - - +
750A ILE* 4.1 1.8 - - - +
752A SER* 1.3 82.9 - - - +
754A VAL* 1.3 65.0 + - - +
756A GLY 3.8 1.4 + - - -
791A ARG* 3.1 33.9 + - - +
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Residues in contact with VAL 754 (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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726A ALA* 4.4 9.2 - - + -
729A TYR* 3.9 35.0 - - + -
730A LEU* 5.1 2.0 - - + -
750A ILE* 2.9 28.3 + - + +
753A GLN* 1.3 71.2 - - - +
755A ALA* 1.3 57.3 + - - +
784A PHE* 3.8 14.8 - - + -
787A GLY 3.4 4.5 - - - +
788A ALA* 3.5 8.0 - - + -
791A ARG* 3.4 23.6 - - - +
793A VAL* 4.1 19.9 - - + +
801A LEU* 3.7 31.6 - - + -
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Residues in contact with ALA 755 (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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751A ALA 3.2 18.0 + - - +
754A VAL* 1.3 77.8 - - - +
756A GLY* 1.3 58.8 + - - +
757A TYR* 3.2 17.1 + - + -
783A ARG 5.0 1.7 - - - +
784A PHE* 3.5 39.0 - - + +
787A GLY* 3.2 31.0 - - - -
788A ALA 4.0 1.3 - - - +
791A ARG* 4.8 0.2 - - - +
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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