Contacts of the helix formed by residues 750 - 769 (chain A) in PDB entry 6DMY
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 LYS 750 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743A PHE* 4.3 35.3 + - + +
744A LEU* 4.3 12.8 - - + +
746A LYS* 3.4 43.1 - - + +
747A PRO 5.9 0.9 - - - +
748A LYS* 3.8 1.0 - - - +
749A ALA* 1.3 81.7 - - - +
751A VAL* 1.3 63.2 + - - +
752A VAL* 3.1 4.2 - - - +
753A VAL* 3.3 37.9 + - + +
754A ILE* 3.8 8.8 + - - +
1173A VAL* 4.1 21.5 - - + +
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Residues in contact with VAL 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A LYS 5.1 9.2 - - - +
749A ALA* 3.1 4.4 - - - -
750A LYS* 1.3 78.1 - - - +
752A VAL* 1.3 58.0 + - - +
754A ILE* 3.0 24.8 + - + +
755A PHE* 3.0 52.0 + - + -
1177A PHE* 6.4 1.6 - - + -
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Residues in contact with VAL 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A ALA* 3.6 17.3 - - + +
750A LYS* 4.8 2.9 - - - +
751A VAL* 1.3 77.1 - - + +
753A VAL* 1.3 57.3 + - + +
755A PHE* 3.0 17.9 + - + +
756A LEU* 2.9 37.7 + - + +
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Residues in contact with VAL 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A LYS* 3.3 39.0 + - + +
751A VAL 3.2 0.6 - - - -
752A VAL* 1.3 76.3 - - + +
754A ILE* 1.3 59.5 + - - +
756A LEU* 3.0 33.4 + - + +
757A PHE* 3.0 34.6 + - + -
1169A VAL* 4.5 11.2 - - + -
1170A LEU* 5.3 1.8 - - + -
1173A VAL* 4.2 26.9 - - + -
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Residues in contact with ILE 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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750A LYS 4.0 7.6 - - - +
751A VAL* 3.0 34.0 + - + +
753A VAL* 1.3 74.8 - - + +
755A PHE* 1.3 56.3 + - + +
757A PHE* 3.4 6.9 + - + +
758A LEU* 2.9 46.0 + - + +
1170A LEU* 5.5 8.7 - - + -
1173A VAL* 4.8 12.8 - - + +
1174A LEU* 6.3 2.9 - - - -
1177A PHE* 6.1 7.4 - - + -
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Residues in contact with PHE 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A VAL* 3.0 50.8 + - + -
752A VAL* 3.0 16.4 + - + +
754A ILE* 1.3 75.3 - - + +
756A LEU* 1.3 58.7 + - - +
758A LEU* 3.7 22.0 - - + +
759A GLY* 3.0 24.1 + - - -
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Residues in contact with LEU 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A VAL* 2.9 27.2 + - + +
753A VAL* 3.0 22.6 + - + +
755A PHE* 1.3 76.8 - - - +
757A PHE* 1.3 69.3 + - + +
759A GLY* 3.3 2.5 + - - -
760A LEU* 3.0 27.2 + - - +
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Residues in contact with PHE 757 (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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753A VAL* 3.0 27.0 + - + +
754A ILE* 4.2 4.5 - - + +
755A PHE 3.3 0.2 - - - -
756A LEU* 1.3 84.7 - - + +
758A LEU* 1.3 60.8 + - - +
760A LEU* 3.9 19.2 - - + +
761A LEU* 2.9 29.9 + - - +
1066A GLU* 4.2 5.6 - - - +
1165A LEU* 3.7 44.9 - - + -
1166A ASN* 4.7 6.5 - - - -
1169A VAL* 4.2 8.5 - - + -
1170A LEU* 3.5 51.4 - - + -
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Residues in contact with LEU 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A ILE* 2.9 34.3 + - + +
755A PHE* 3.7 28.9 - - + +
756A LEU 3.3 0.2 - - - -
757A PHE* 1.3 76.4 - - - +
759A GLY* 1.3 57.1 + - - +
761A LEU* 3.3 11.4 + - + +
762A GLY* 2.9 25.5 + - - -
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Residues in contact with GLY 759 (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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755A PHE 3.0 14.9 + - - -
756A LEU* 3.3 3.3 + - - -
758A LEU* 1.3 76.6 - - - +
760A LEU* 1.3 56.2 + - - +
762A GLY* 3.3 2.2 + - - -
763A VAL* 3.0 35.2 + - - +
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Residues in contact with LEU 760 (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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756A LEU 3.0 15.8 + - - +
757A PHE* 4.2 21.5 - - + +
759A GLY* 1.3 76.0 - - - +
761A LEU* 1.3 57.7 + - - +
763A VAL* 3.8 8.9 - - + +
764A SER* 3.0 29.8 + - - -
1066A GLU* 3.5 33.9 - - + +
1162A LEU* 4.6 18.2 - - + -
1165A LEU* 5.3 10.3 - - + -
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Residues in contact with LEU 761 (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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757A PHE 2.9 21.7 + - - +
758A LEU* 3.7 12.3 - - + +
760A LEU* 1.3 76.7 - - - +
762A GLY* 1.3 62.0 + - - +
764A SER* 2.5 25.0 + - - +
765A LEU* 2.9 44.6 + - + +
1062A LEU* 3.7 30.7 - - + -
1065A VAL* 4.7 2.9 - - + -
1066A GLU* 3.3 22.9 + - + +
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Residues in contact with GLY 762 (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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758A LEU 2.9 15.5 + - - -
759A GLY* 3.3 2.7 + - - -
761A LEU* 1.3 76.6 - - - +
763A VAL* 1.3 63.9 + - - +
765A LEU* 3.1 6.7 + - - +
766A TYR* 3.0 24.1 + - - +
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Residues in contact with VAL 763 (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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759A GLY 3.0 21.5 + - - +
760A LEU* 3.8 8.3 - - + +
762A GLY* 1.3 73.0 - - - +
764A SER* 1.3 58.6 + - - +
766A TYR* 3.6 5.5 + - - +
767A GLY 3.0 21.0 + - - -
1073A LEU* 3.6 26.6 - - + +
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Residues in contact with SER 764 (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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760A LEU* 3.0 14.1 + - - -
761A LEU* 2.5 32.2 + - - +
763A VAL* 1.3 80.0 - - - +
765A LEU* 1.3 59.3 + - - +
767A GLY* 3.2 2.4 + - - +
768A THR* 2.9 22.7 + - - +
1065A VAL 4.4 0.7 - - - -
1066A GLU* 3.3 40.9 - - - +
1069A GLY* 3.3 10.2 - - - -
1070A MET* 4.7 9.9 - - - +
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Residues in contact with LEU 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A LEU* 2.9 47.4 + - + +
762A GLY* 3.1 6.5 + - - +
764A SER* 1.3 74.8 + - - +
766A TYR* 1.3 61.1 + - - +
767A GLY 3.1 0.9 - - - -
768A THR* 2.3 36.7 + - + +
769A THR* 3.1 7.4 + - - +
1062A LEU* 5.9 0.2 - - + -
1065A VAL* 3.7 28.3 - - + -
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Residues in contact with TYR 766 (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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762A GLY 3.0 15.3 + - - +
763A VAL* 4.0 5.4 - - - +
765A LEU* 1.3 74.6 - - - +
767A GLY* 1.3 62.4 + - - +
769A THR* 3.2 24.5 + - + +
770A ARG* 3.1 50.8 + - + +
1073A LEU* 4.3 13.2 - - + -
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Residues in contact with GLY 767 (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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763A VAL 3.0 12.8 + - - -
764A SER 3.4 4.0 - - - -
765A LEU 3.1 0.6 - - - -
766A TYR* 1.3 78.6 - - - +
768A THR* 1.3 59.5 + - - +
770A ARG* 3.1 10.0 + - - -
771A VAL* 3.3 11.6 - - - +
1069A GLY 3.2 27.7 - - - +
1072A GLY* 3.5 4.3 - - - -
1073A LEU* 3.6 20.6 - - - +
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Residues in contact with THR 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A SER 2.9 20.3 + - - +
765A LEU* 2.3 36.8 + - + +
767A GLY* 1.3 75.8 - - - +
769A THR* 1.3 59.6 + - - +
770A ARG 3.2 1.3 + - - -
771A VAL* 3.5 19.5 + - - +
1065A VAL* 4.1 17.3 - - + +
1068A PHE* 3.9 24.8 - - + -
1069A GLY* 3.7 15.9 - - - +
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Residues in contact with THR 769 (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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765A LEU 3.9 2.7 - - - +
766A TYR* 3.2 39.9 - - + +
768A THR* 1.3 79.9 + - - +
770A ARG* 1.3 62.2 + - - +
771A VAL 3.7 1.1 - - - -
772A ARG* 4.1 13.8 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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