Contacts of the helix formed by residues 837 - 850 (chain A) in PDB entry 4N78
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 GLY 837 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A ASN* 3.1 29.8 - - - -
830A HIS 4.2 0.4 - - - -
831A ASN* 3.6 16.5 + - - +
836A TYR* 1.3 78.4 - - - +
838A ARG* 1.3 65.6 + - - -
839A ILE 3.3 2.5 - - - -
840A THR* 3.7 8.9 + - - -
841A LEU* 3.2 21.9 + - - +
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Residues in contact with ARG 838 (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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781A GLU* 2.8 42.8 + - - +
784A ILE* 3.9 19.1 - - + +
785A GLY* 4.1 6.1 - - - -
788A GLU* 2.7 48.8 + - - +
828A ALA 3.0 25.0 + - - -
829A ASN* 2.7 19.9 + - - +
830A HIS* 3.6 36.0 + - + +
837A GLY* 1.3 71.2 - - - -
839A ILE* 1.3 60.1 + - - +
841A LEU* 3.4 10.1 + - + +
842A HIS* 2.9 31.4 + - - +
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Residues in contact with ILE 839 (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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784A ILE* 4.5 15.3 - - + -
787A PHE* 3.8 21.3 - - + -
795A ILE* 4.6 1.3 - - + -
798A LEU* 3.8 21.8 - - + -
802A LEU* 4.4 5.4 - - + -
825A PHE* 3.6 36.3 - - + -
829A ASN* 2.9 19.8 + - - +
837A GLY 3.3 0.2 - - - -
838A ARG* 1.3 74.6 - - - +
840A THR* 1.3 62.2 + - - +
842A HIS* 3.2 2.4 + - - +
843A VAL* 2.9 41.1 + - + +
920A LEU* 4.0 36.8 - - + +
921A LEU* 4.8 1.1 - - + -
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Residues in contact with THR 840 (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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829A ASN* 5.7 0.9 + - - -
836A TYR* 4.3 11.6 - - + -
837A GLY* 3.7 17.9 + - - -
839A ILE* 1.3 78.7 - - - +
841A LEU* 1.3 65.2 + - + +
843A VAL* 3.3 4.5 + - - +
844A PHE* 3.1 22.0 + - + +
920A LEU 4.3 3.6 + - - -
921A LEU* 3.6 36.8 + - + +
925A GLY* 4.0 24.5 - - - +
928A VAL* 4.2 15.3 - - + -
929A VAL* 4.7 3.2 - - + +
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Residues in contact with LEU 841 (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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836A TYR* 4.0 30.7 - - + +
837A GLY 3.2 19.7 + - - +
838A ARG* 3.8 9.6 - - + +
839A ILE 3.3 0.6 - - - -
840A THR* 1.3 79.2 - - + +
842A HIS* 1.3 57.7 + - - +
844A PHE* 3.4 12.3 + - + +
845A TRP* 3.0 27.3 + - - +
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Residues in contact with HIS 842 (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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787A PHE* 2.7 57.6 + + + -
788A GLU* 3.1 38.0 + - + +
790A GLU 3.0 12.4 + - - -
838A ARG 2.9 18.1 + - - +
839A ILE 3.8 3.4 - - - +
841A LEU* 1.3 74.0 - - - +
843A VAL* 1.3 60.2 + - - +
845A TRP* 4.1 14.9 - + - +
846A GLU* 2.9 58.4 + - + +
877A ARG* 5.0 0.9 - - - -
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Residues in contact with VAL 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A PHE* 4.0 8.3 - - + -
792A LEU* 4.1 20.4 - - + +
795A ILE* 4.0 23.8 - - + -
839A ILE* 2.9 20.2 + - + +
840A THR 3.3 8.5 + - - +
842A HIS* 1.3 78.0 - - - +
844A PHE* 1.3 57.1 + - - +
846A GLU* 3.8 2.1 - - - +
847A LEU* 3.0 41.2 + - + +
917A ILE* 4.3 18.6 - - + -
921A LEU* 3.9 26.7 - - + -
929A VAL* 5.0 1.3 - - + -
1006A PHE* 5.0 1.1 - - + -
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Residues in contact with PHE 844 (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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840A THR* 3.1 10.4 + - + +
841A LEU* 3.7 14.8 - - + +
843A VAL* 1.3 78.8 - - - +
845A TRP* 1.3 68.6 + + - +
847A LEU* 3.2 12.9 + - + +
848A ASN* 3.0 52.2 + - + +
929A VAL* 4.6 22.2 - - + -
932A GLU* 3.2 54.3 - - + -
933A LEU* 4.7 6.1 - - + -
936A VAL* 4.8 2.0 - - + -
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Residues in contact with TRP 845 (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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841A LEU 3.0 17.4 + - - +
842A HIS* 3.3 16.8 + + - +
844A PHE* 1.3 83.2 - + + +
846A GLU* 1.3 74.4 + - - +
848A ASN* 3.4 2.5 + - - +
849A TYR* 3.1 79.2 + + + +
875A PHE* 4.0 29.5 - + - -
877A ARG* 6.1 2.4 - - - +
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Residues in contact with GLU 846 (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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790A GLU 3.7 7.2 - - - -
791A ASP* 3.5 6.3 - - - +
792A LEU* 3.9 26.6 + - + +
842A HIS* 2.9 47.3 + - + +
843A VAL* 3.8 5.2 - - - +
845A TRP* 1.3 84.6 + - - +
847A LEU* 1.3 62.3 + - - +
849A TYR* 4.5 1.6 - - - +
850A ASP* 2.8 38.8 + - + +
851A PHE* 3.0 10.9 + - - -
877A ARG* 2.7 43.9 + - - +
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Residues in contact with LEU 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A LEU* 4.0 10.5 - - + -
843A VAL* 3.0 30.4 + - + +
844A PHE* 3.2 13.7 + - + +
846A GLU* 1.3 75.6 - - - +
848A ASN* 1.3 61.3 + - - +
851A PHE* 3.7 29.3 + - + -
852A LEU* 3.1 40.1 + - + +
929A VAL* 3.6 30.1 - - + -
933A LEU* 4.6 13.0 - - + -
1006A PHE* 3.6 39.0 - - + -
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Residues in contact with ASN 848 (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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844A PHE* 3.0 39.4 + - + +
845A TRP* 3.7 5.6 - - - +
846A GLU 3.2 0.2 - - - -
847A LEU* 1.3 79.7 - - - +
849A TYR* 1.3 75.5 - - + +
852A LEU* 4.7 7.1 - - - +
853A PRO* 4.0 10.8 - - - +
933A LEU* 5.7 1.2 - - - +
936A VAL* 3.5 34.0 - - - +
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Residues in contact with TYR 849 (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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845A TRP* 3.1 77.7 + + + +
846A GLU* 5.2 1.3 - - - +
848A ASN* 1.3 93.0 - - + +
850A ASP* 1.3 61.1 + - + +
853A PRO* 3.7 12.4 - - - +
854A ASN* 4.0 6.6 + - - -
873A GLN* 4.3 7.6 - - - +
875A PHE* 4.3 42.3 - + + +
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Residues in contact with ASP 850 (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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791A ASP* 3.6 13.7 - - - +
792A LEU* 4.9 2.8 + - + +
846A GLU* 2.8 25.6 + - + +
848A ASN 3.6 1.2 - - - -
849A TYR* 1.3 80.7 - - + +
851A PHE* 1.3 66.4 + - - +
853A PRO* 3.2 2.6 - - - +
854A ASN* 2.9 50.8 + - - +
855A TYR* 3.8 7.0 - - - -
866A ARG* 2.8 37.4 + - - -
873A GLN 5.0 0.2 - - - +
877A ARG* 4.1 9.6 - - - +
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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