Contacts of the helix formed by residues 867 - 879 (chain S) in PDB entry 1NVU
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 867 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789S THR* 3.0 47.2 + - + +
792S GLU* 3.0 22.6 + - - +
862S PHE* 2.9 27.1 + - + +
865S LEU* 3.1 1.5 - - + +
866S ASN* 1.3 75.6 - - - +
868S PHE* 1.3 56.0 + - - +
869S ASN* 3.2 5.2 + - - +
870S GLY* 2.7 23.5 + - - -
871S VAL* 3.1 29.7 + - - +
927S VAL* 3.3 21.7 - - + +
979S TYR* 4.2 0.7 - - - -
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Residues in contact with PHE 868 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863S GLN* 4.6 6.7 - - - -
866S ASN* 3.2 27.8 + - + -
867S ASN* 1.3 70.0 - - - +
869S ASN* 1.3 66.6 + - - +
871S VAL* 3.4 8.0 + - + +
872S LEU* 3.0 30.0 + - + +
907S LEU* 4.8 10.3 - - + -
915S TYR* 3.5 32.5 - + + -
918S LYS* 3.8 41.5 - - + -
919S LEU* 3.7 34.1 - - + -
922S ILE* 4.0 24.2 - - + -
926S CYS* 4.2 2.0 - - + -
927S VAL 2.8 16.3 + - - +
928S PRO* 4.5 0.2 - - + -
929S PHE 4.3 5.2 - - - +
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Residues in contact with ASN 869 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R TYR* 4.7 2.3 + - - -
792S GLU* 3.1 28.9 + - - +
824S MET* 4.7 11.2 - - - +
828S THR* 3.0 34.8 + - - +
867S ASN* 3.2 6.7 + - - +
868S PHE* 1.3 77.3 - - - +
870S GLY* 1.3 62.6 + - - +
872S LEU* 3.4 3.5 + - - +
873S GLU* 3.0 37.5 + - - +
927S VAL* 3.1 15.4 + - + -
928S PRO 3.7 17.8 + - - +
929S PHE* 4.3 18.8 - - - +
930S PHE 5.1 0.7 + - - -
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Residues in contact with GLY 870 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792S GLU* 3.4 8.2 + - - -
862S PHE* 3.3 31.3 - - - -
867S ASN* 2.7 16.5 + - - -
869S ASN* 1.3 78.3 - - - +
871S VAL* 1.3 60.4 + - - +
873S GLU* 3.2 26.3 + - - +
874S VAL* 3.3 9.7 + - - +
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Residues in contact with VAL 871 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859S LEU* 4.1 9.4 - - + +
862S PHE* 3.8 15.4 - - + -
863S GLN* 3.5 36.3 - - + +
867S ASN 3.1 19.4 + - - +
868S PHE* 3.7 12.6 - - + +
869S ASN 3.3 0.2 - - - -
870S GLY* 1.3 75.3 - - - +
872S LEU* 1.3 63.0 + - + +
874S VAL* 3.2 5.7 + - - +
875S VAL* 3.0 27.3 + - + +
904S ALA* 3.9 26.2 - - + -
907S LEU* 4.3 17.3 - - + -
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Residues in contact with LEU 872 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67R MET* 4.9 7.9 - - + -
70R GLN* 5.9 0.9 - - - +
828S THR* 6.0 0.4 - - - -
868S PHE* 3.0 14.2 + - + +
869S ASN 4.1 2.9 - - - +
871S VAL* 1.3 83.6 - - + +
873S GLU* 1.3 57.3 + - - +
875S VAL* 3.9 14.5 - - + +
876S SER* 2.7 42.0 + - - +
904S ALA 4.7 8.1 - - - +
907S LEU* 5.1 8.5 - - + -
908S SER* 4.8 9.2 - - - -
912S TYR* 3.8 23.3 - - + +
915S TYR* 5.0 7.9 - - + -
929S PHE* 3.5 48.9 - - + -
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Residues in contact with GLU 873 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792S GLU* 2.8 22.5 - - - +
827S HIS* 3.6 4.0 + - - -
828S THR* 3.1 44.3 + - + +
831S LEU* 2.8 33.5 - - + +
832S THR* 3.3 21.9 + - - +
835S PHE* 4.3 6.4 - - + -
862S PHE* 4.3 1.4 - - - -
869S ASN* 3.0 31.9 + - - +
870S GLY* 3.2 15.0 + - - +
872S LEU* 1.3 75.1 - - - +
874S VAL* 1.3 63.2 + - - +
876S SER* 4.5 0.7 - - - -
877S ALA* 3.2 21.3 + - - +
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Residues in contact with VAL 874 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835S PHE* 3.7 28.9 - - + -
855S ILE* 3.8 28.3 - - + +
856S ILE* 5.1 1.1 - - - -
858S ILE* 5.1 0.2 - - + -
859S LEU* 3.6 37.5 - - + +
862S PHE* 4.2 8.3 - - + -
870S GLY 3.3 10.5 + - - +
871S VAL 3.2 7.3 + - - +
872S LEU 3.2 0.4 - - - -
873S GLU* 1.3 76.0 - - - +
875S VAL* 1.3 66.5 + - - +
877S ALA* 3.1 4.1 + - - +
878S MET* 2.9 34.8 + - + +
901S LEU* 4.7 0.9 - - + -
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Residues in contact with VAL 875 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R GLN* 3.4 16.6 - - - +
859S LEU* 4.3 5.4 - - + -
871S VAL* 3.0 19.4 + - + +
872S LEU* 3.9 12.8 - - + +
874S VAL* 1.3 75.8 - - - +
876S SER* 1.3 62.7 + - - +
878S MET* 3.3 4.7 + - - -
879S ASN* 2.9 47.2 + - - +
901S LEU* 4.6 6.3 - - + -
904S ALA* 3.6 37.0 - - + +
905S HIS* 3.8 20.6 - - + +
908S SER* 5.2 0.7 - - - +
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Residues in contact with SER 876 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R ALA 4.1 9.7 - - - +
67R MET* 3.3 36.3 - - - +
70R GLN* 3.4 20.1 + - - +
832S THR* 3.9 15.7 - - - -
872S LEU* 2.7 26.4 + - - +
873S GLU* 3.8 4.9 - - - -
875S VAL* 1.3 74.0 - - - +
877S ALA* 1.3 62.0 + - - +
879S ASN* 3.4 2.1 + - - +
880S SER* 3.1 22.7 + - - -
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Residues in contact with ALA 877 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832S THR* 3.5 28.0 - - + +
835S PHE* 3.8 18.4 - - + -
836S GLU* 3.9 11.0 - - + +
839S ILE* 5.7 1.1 - - + -
873S GLU 3.2 11.0 + - - +
874S VAL* 3.1 10.1 + - - +
876S SER* 1.3 77.7 - - - +
878S MET* 1.3 67.0 + - + +
880S SER* 2.8 23.6 + - - -
883S VAL* 3.4 12.1 - - + +
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Residues in contact with MET 878 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839S ILE* 4.2 13.5 - - + -
852S VAL* 4.1 17.9 - - + +
855S ILE* 3.5 38.8 - - + -
856S ILE* 4.3 6.5 - - + -
874S VAL* 2.9 23.0 + - + +
875S VAL 3.8 3.6 - - - +
877S ALA* 1.3 77.7 - - + +
879S ASN* 1.3 63.4 + - - +
883S VAL* 3.9 11.9 - - - +
884S TYR* 3.5 26.5 + - - +
890S PHE* 3.8 29.1 - - + -
901S LEU* 3.7 35.0 - - + -
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Residues in contact with ASN 879 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R ASP* 4.0 7.0 - - - +
70R GLN* 3.8 22.6 + - + -
73R ARG* 2.7 36.5 + - - +
875S VAL* 2.9 44.5 + - - +
876S SER 3.7 2.2 - - - +
878S MET* 1.3 81.6 - - - +
880S SER* 1.3 62.2 + - - +
884S TYR* 3.6 22.5 - - - -
901S LEU* 5.6 2.4 - - - +
905S HIS* 3.6 29.5 + - - +
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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