Contacts of the helix formed by residues 958 - 976 (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 PHE 958 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601S ILE* 3.8 26.2 - - + +
602S LYS 3.0 12.3 + - - +
603S ALA* 4.4 0.4 - - - -
609S LEU* 4.2 22.7 - - + -
623S PHE* 3.6 41.7 - + - -
626S THR* 3.7 33.2 - - + -
627S PHE* 4.4 24.2 - + - -
630S THR* 4.7 0.4 - - - -
634S PHE* 4.7 7.9 - + - -
956S ILE* 3.0 10.4 + - + +
957S ASN* 1.3 71.3 - - - +
959S SER* 1.3 61.2 + - - +
960S LYS 3.1 2.5 - - - -
961S ARG* 3.0 16.9 + - + +
962S ARG* 2.9 34.9 + - + +
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Residues in contact with SER 959 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R GLU* 3.3 40.2 + - - +
589S GLU* 3.9 1.6 - - - -
602S LYS* 3.0 11.3 + - - +
944S ASN* 5.6 0.5 + - - -
957S ASN* 2.8 21.4 + - - -
958S PHE* 1.3 77.1 - - - +
960S LYS* 1.3 62.4 + - - +
962S ARG* 3.2 32.5 + - - +
963S LYS* 3.1 31.4 + - - +
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Residues in contact with LYS 960 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940S THR* 3.8 6.9 - - + +
941S GLU* 2.9 45.5 + - - +
944S ASN* 2.8 39.6 + - + +
945S PRO 3.6 8.3 - - - +
946S GLU* 2.6 36.3 + - - +
957S ASN* 3.5 22.6 + - - +
958S PHE 3.1 0.6 - - - -
959S SER* 1.3 82.8 + - - +
961S ARG* 1.3 68.0 + - - +
963S LYS* 3.3 13.6 + - - +
964S VAL* 3.2 24.6 + - + +
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Residues in contact with ARG 961 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626S THR* 3.8 1.7 - - + +
630S THR* 3.2 38.1 - - - +
633S SER* 3.0 29.5 + - - -
634S PHE* 3.7 33.7 - - + +
946S GLU* 2.9 57.5 + - - +
956S ILE* 3.8 1.8 - - - +
957S ASN* 2.9 26.7 + - - +
958S PHE* 3.0 18.2 + - + +
960S LYS* 1.3 80.2 - - - +
962S ARG* 1.3 64.4 + - - +
964S VAL* 3.2 6.2 + - - +
965S ALA* 3.0 25.1 + - - +
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Residues in contact with ARG 962 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R GLU* 4.8 1.2 + - - -
589S GLU* 3.1 28.5 + - - +
600S ILE* 3.6 27.3 - - - +
601S ILE 2.9 25.8 + - - +
622S ASN* 5.9 5.4 - - - +
626S THR* 3.9 19.4 + - + +
958S PHE* 2.9 21.4 + - + +
959S SER* 3.2 25.1 + - - +
960S LYS 3.3 0.2 - - - -
961S ARG* 1.3 75.4 - - - +
963S LYS* 1.3 61.2 + - + +
965S ALA* 3.4 1.6 + - - +
966S GLU* 2.9 48.4 + - - +
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Residues in contact with LYS 963 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R GLU* 3.1 32.3 + - - +
32R TYR 3.2 38.6 - - - +
33R ASP* 3.9 24.0 + - - +
940S THR* 3.6 22.2 - - + +
944S ASN* 4.3 5.2 - - - +
959S SER* 3.1 19.9 + - - +
960S LYS* 3.5 10.1 - - - +
961S ARG 3.2 0.2 - - - -
962S ARG* 1.3 79.5 - - + +
964S VAL* 1.3 62.2 + - - +
966S GLU* 3.3 24.6 + - - +
967S ILE* 3.4 18.5 + - - +
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Residues in contact with VAL 964 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630S THR* 4.7 7.4 - - + -
805S VAL* 4.4 17.7 - - + -
937S ILE* 4.4 17.3 - - + -
940S THR* 4.0 11.0 - - + -
941S GLU* 3.7 37.7 - - + +
960S LYS* 3.2 16.0 + - + +
961S ARG* 3.2 10.3 + - - +
963S LYS* 1.3 75.7 - - - +
965S ALA* 1.3 58.9 + - - +
967S ILE* 3.0 14.0 + - - +
968S THR* 2.9 36.4 + - + +
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Residues in contact with ALA 965 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625S ARG* 2.8 32.5 + - - +
626S THR* 3.5 37.9 - - + +
629S THR* 5.1 2.5 - - - -
630S THR* 4.6 7.0 - - + -
961S ARG 3.0 16.4 + - - +
962S ARG 3.9 2.5 - - - +
964S VAL* 1.3 75.9 - - - +
966S GLU* 1.3 60.2 + - - +
967S ILE 3.2 0.2 - - - -
968S THR* 3.3 10.5 - - - +
969S GLY 2.9 11.8 + - - -
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Residues in contact with GLU 966 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R ASP* 5.7 1.0 - - - +
622S ASN* 5.5 3.8 + - - -
625S ARG* 4.8 4.3 - - - +
962S ARG* 2.9 40.5 + - - +
963S LYS* 3.5 19.7 - - - +
964S VAL 3.2 0.2 - - - -
965S ALA* 1.3 78.0 - - - +
967S ILE* 1.3 60.6 + - + +
969S GLY* 3.5 1.0 + - - -
970S GLU* 3.1 27.2 + - - +
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Residues in contact with ILE 967 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35R THR* 4.6 13.0 - - + -
933S TYR* 3.9 30.5 - - + +
936S ASN* 3.8 32.3 - - + +
937S ILE* 3.6 37.7 - - + -
940S THR* 4.1 8.3 - - - +
963S LYS* 3.5 14.1 - - + +
964S VAL* 3.0 8.9 + - - +
966S GLU* 1.3 76.1 - - + +
968S THR* 1.3 65.5 + - - +
970S GLU* 3.1 8.0 + - - +
971S ILE* 3.1 22.1 + - + +
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Residues in contact with THR 968 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625S ARG* 3.7 5.9 + - - -
629S THR* 4.2 11.6 + - + +
801S PRO* 4.5 24.5 - - + -
804S LEU* 4.3 24.5 - - + -
805S VAL* 4.8 2.0 - - + -
937S ILE* 4.4 6.5 - - + -
964S VAL* 2.9 26.6 + - + +
965S ALA* 3.2 18.5 + - - +
967S ILE* 1.3 75.6 - - - +
969S GLY* 1.3 58.6 + - - +
971S ILE* 3.3 11.2 + - - +
972S GLN* 2.9 35.3 + - - +
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Residues in contact with GLY 969 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Q ARG* 6.0 0.5 - - - +
625S ARG* 3.6 19.7 - - - -
965S ALA 2.9 20.3 + - - -
966S GLU* 3.8 1.6 - - - -
968S THR* 1.3 75.3 + - - +
970S GLU* 1.3 59.1 + - - +
972S GLN* 3.2 9.0 + - - +
973S GLN* 3.0 27.5 + - - +
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Residues in contact with GLU 970 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916S LEU* 5.8 3.5 - - - +
919S LEU* 4.0 8.3 - - - +
920S ARG* 6.0 1.8 - - - +
933S TYR* 2.9 36.2 + - + +
966S GLU 3.1 13.9 + - - +
967S ILE* 3.1 10.1 + - - +
969S GLY* 1.3 72.6 - - - +
971S ILE* 1.3 67.6 + - - +
973S GLN* 3.3 13.8 + - - +
974S TYR* 3.3 33.4 + - + -
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Residues in contact with ILE 971 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796S TYR* 2.8 29.6 + - + +
799S VAL 5.1 2.2 - - - +
804S LEU* 3.6 30.5 - - + -
930S PHE* 3.9 26.0 - - + -
933S TYR* 3.5 37.9 - - + -
937S ILE* 4.6 1.1 - - + -
967S ILE* 3.1 22.6 + - + +
968S THR* 3.4 11.9 - - - +
970S GLU* 1.3 77.1 - - - +
972S GLN* 1.3 63.7 + - + +
974S TYR 3.2 7.1 + - - -
975S GLN* 3.3 26.6 + - - +
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Residues in contact with GLN 972 (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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625S ARG* 3.9 26.7 + - - +
629S THR* 5.4 1.4 + - - -
799S VAL 6.0 0.2 - - - +
800S GLN* 5.5 1.8 + - - -
801S PRO* 3.6 32.5 - - + +
968S THR* 2.9 26.1 + - - +
969S GLY* 3.2 5.7 + - - +
971S ILE* 1.3 74.9 - - + +
973S GLN* 1.3 65.6 + - - +
975S GLN* 2.9 33.6 + - - +
976S ASN* 3.5 15.0 + - - +
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Residues in contact with GLN 973 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Q ARG* 3.4 40.6 - - + +
42Q LYS* 3.8 1.8 - - - +
43Q GLN* 3.0 27.7 + - - +
52Q LEU* 5.1 3.2 - - + +
969S GLY 3.0 13.5 + - - +
970S GLU* 3.6 10.5 - - - +
971S ILE 3.3 0.6 - - - -
972S GLN* 1.3 76.8 - - - +
974S TYR* 1.3 97.4 + - - +
975S GLN 3.4 0.5 + - - -
976S ASN* 3.5 15.3 + - - +
977S GLN* 2.9 46.0 + - - +
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Residues in contact with TYR 974 (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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1Q MET* 5.3 0.3 - - - +
43Q GLN* 2.5 36.3 + - - -
796S TYR* 3.5 22.6 - - + +
797S ARG* 5.1 1.4 - - - +
919S LEU* 3.5 26.5 + - + +
920S ARG* 4.3 5.4 - - - +
922S ILE* 5.1 0.2 - - + -
924S PRO* 4.4 9.9 - - + -
926S CYS* 3.4 35.3 + - - +
928S PRO* 3.8 17.0 - - + -
933S TYR* 3.7 22.0 - - - -
970S GLU* 3.3 37.0 + - + -
971S ILE 3.2 2.2 + - - -
972S GLN 3.2 0.2 - - - -
973S GLN* 1.3 96.7 - - - +
975S GLN* 1.3 60.6 + - - +
976S ASN 3.3 0.4 - - - -
977S GLN* 3.5 13.9 + - - +
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Residues in contact with GLN 975 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796S TYR* 2.9 39.8 + - + -
797S ARG* 2.8 49.4 + - + +
799S VAL* 2.8 29.3 + - - +
800S GLN* 5.7 0.7 + - - -
801S PRO* 6.0 0.2 - - - +
971S ILE* 3.3 24.3 - - - +
972S GLN* 2.9 33.6 + - - +
974S TYR* 1.3 78.1 - - - +
976S ASN* 1.3 58.9 + - - +
977S GLN 3.7 0.2 - - - -
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Residues in contact with ASN 976 (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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24Q ILE* 3.3 39.4 - - + +
25Q GLN* 3.1 38.5 + - + +
40Q TYR* 5.9 0.6 - - - -
41Q ARG 4.1 9.1 + - - +
797S ARG* 3.2 12.0 + - - -
972S GLN 3.5 16.4 + - - +
973S GLN* 3.6 18.8 + - - +
974S TYR 3.3 1.8 - - - -
975S GLN* 1.3 81.9 - - - +
977S GLN* 1.3 62.6 + - - +
978S PRO* 3.2 9.2 - - - +
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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
------------------------------------------------------------
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