Contacts of the helix formed by residues 930 - 943 (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 930 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64R TYR* 3.3 15.3 + - - +
796S TYR* 3.7 38.6 - + - -
799S VAL* 3.8 36.8 - - + -
804S LEU* 4.0 7.0 - - + -
821S LEU* 3.8 7.0 - - + -
824S MET* 3.4 23.3 - - + -
869S ASN* 5.1 1.2 + - - -
928S PRO 3.6 4.2 + - - +
929S PHE* 1.3 74.6 - - - +
931S GLY* 1.3 67.4 + - - +
933S TYR* 3.0 22.6 + + + +
934S LEU* 3.2 32.0 + - + +
971S ILE* 3.9 35.7 - - + -
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Residues in contact with GLY 931 (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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61R GLN* 3.4 28.2 - - - +
64R TYR* 3.4 15.1 + - - -
929S PHE* 3.4 22.9 - - - -
930S PHE* 1.3 76.2 - - - +
932S ILE* 1.3 62.0 + - - +
934S LEU* 3.1 5.2 + - - +
935S THR* 3.1 19.6 + - - -
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Residues in contact with ILE 932 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R GLN* 4.7 6.7 - - - +
911S HIS 5.5 0.2 - - - +
912S TYR* 3.1 49.6 - - + -
915S TYR* 4.3 14.8 - - + -
916S LEU* 4.4 21.5 - - + -
929S PHE* 3.7 23.2 - - + +
930S PHE 3.1 0.6 + - - -
931S GLY* 1.3 74.9 - - - +
933S TYR* 1.3 73.2 + - + +
935S THR* 3.4 3.9 + - - -
936S ASN* 3.1 39.4 + - - +
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Residues in contact with TYR 933 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796S TYR* 4.2 6.7 - + - -
915S TYR* 5.5 0.9 - + - -
916S LEU* 6.5 1.1 - - + -
919S LEU* 3.7 11.2 - - + +
928S PRO* 4.0 19.5 - - + +
929S PHE 4.0 4.9 - - - -
930S PHE* 3.0 29.1 + + + +
932S ILE* 1.3 85.5 - - + +
934S LEU* 1.3 57.2 + - - +
936S ASN* 3.3 5.6 + - - +
937S ILE* 2.9 36.3 + - + +
967S ILE* 3.9 18.3 - - + +
970S GLU* 2.9 44.9 + - + +
971S ILE* 3.5 37.7 - - + -
974S TYR* 3.7 15.4 - - - -
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Residues in contact with LEU 934 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60R GLY* 3.6 21.5 - - - +
64R TYR* 4.2 15.9 - - + +
804S LEU* 3.9 9.9 - - + -
809S TRP* 3.3 37.6 - - + +
821S LEU* 3.8 22.7 - - + -
825S ILE* 4.0 26.7 - - + -
930S PHE* 3.5 33.4 - - + +
931S GLY* 3.1 6.2 + - - +
933S TYR* 1.3 74.8 - - - +
935S THR* 1.3 57.7 + - - +
937S ILE* 4.7 1.3 - - + -
938S LEU* 3.0 26.2 + - - +
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Residues in contact with THR 935 (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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57R ASP 3.9 10.1 - - - +
58R THR 4.2 0.9 - - - -
59R GLY 3.0 26.1 + - - +
61R GLN* 2.8 30.7 + - - +
931S GLY 3.1 5.5 + - - -
932S ILE* 3.8 8.3 - - - -
934S LEU* 1.3 77.4 - - - +
936S ASN* 1.3 61.2 + - - +
938S LEU* 3.4 1.6 + - - +
939S LYS* 3.0 61.0 + - + +
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Residues in contact with ASN 936 (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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34R PRO* 3.5 23.5 - - - +
35R THR* 3.9 26.2 - - + +
916S LEU* 6.3 0.8 - - - +
932S ILE* 3.1 36.8 + - - +
933S TYR* 3.8 6.8 - - - +
935S THR* 1.3 83.3 - - - +
937S ILE* 1.3 60.7 + - - +
939S LYS* 4.7 1.8 + - - +
940S THR* 2.8 30.3 + - - -
967S ILE* 3.8 17.9 - - + +
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Residues in contact with ILE 937 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804S LEU* 4.0 52.7 - - + +
809S TRP* 4.1 10.3 - - + -
933S TYR* 2.9 23.2 + - + +
934S LEU* 3.9 3.8 - - + +
936S ASN* 1.3 73.4 - - - +
938S LEU* 1.3 67.7 + - - +
940S THR* 3.3 3.9 + - - -
941S GLU* 3.0 38.6 + - + +
964S VAL* 4.4 13.7 - - + -
967S ILE* 3.6 34.8 - - + -
968S THR* 4.4 9.2 - - + -
971S ILE* 4.6 1.3 - - + -
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Residues in contact with LEU 938 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R SER* 3.6 17.3 - - - +
59R GLY 3.5 6.7 - - - -
60R GLY* 3.5 31.6 - - - +
1003R PO4 3.8 14.6 - - - +
807S SER* 3.4 32.1 - - - +
809S TRP* 4.2 5.1 - - + -
810S THR* 4.5 11.4 - - + +
934S LEU 3.0 18.5 + - - +
935S THR 3.8 3.8 - - - +
937S ILE* 1.3 78.0 - - - +
939S LYS* 1.3 56.0 + - - +
941S GLU* 3.3 2.3 + - - +
942S GLU* 2.9 53.8 + - + +
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Residues in contact with LYS 939 (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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17R SER* 4.2 12.1 - - - +
20R THR* 4.9 11.2 - - - +
21R ILE* 3.5 25.0 - - + +
32R TYR* 3.5 12.5 - - + +
34R PRO* 3.7 26.7 - - + -
40R TYR* 5.8 6.5 - - - +
55R ILE 5.8 1.2 + - - -
57R ASP* 2.8 41.5 + - - +
935S THR* 3.0 37.9 + - + +
936S ASN* 5.1 1.5 + - - +
938S LEU* 1.3 74.5 - - + +
940S THR* 1.3 61.6 + - - +
942S GLU* 4.7 0.7 - - - -
943S GLY* 2.8 27.4 + - - -
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Residues in contact with THR 940 (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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32R TYR 4.8 0.4 - - - +
33R ASP* 5.1 0.3 + - - -
34R PRO* 3.2 18.7 - - - +
35R THR* 5.3 0.7 - - - +
936S ASN 2.8 23.4 + - - -
937S ILE* 3.3 6.9 + - - -
939S LYS* 1.3 77.3 - - - +
941S GLU* 1.3 62.3 + - - +
944S ASN* 2.8 42.9 + - - +
960S LYS* 3.8 13.1 - - + +
963S LYS* 3.6 32.1 - - + +
964S VAL* 4.0 11.9 - - + +
967S ILE* 4.1 8.8 - - - +
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Residues in contact with GLU 941 (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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805S VAL* 4.4 4.3 - - - +
806S GLY* 3.1 20.8 + - - -
807S SER* 2.8 42.4 + - - +
937S ILE* 3.0 22.3 + - - +
938S LEU 3.8 2.9 - - - +
940S THR* 1.3 79.4 - - - +
942S GLU* 1.3 61.2 + - + +
944S ASN 3.6 2.3 - - - +
960S LYS* 2.9 34.4 + - - +
964S VAL* 3.7 29.7 - - + +
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Residues in contact with GLU 942 (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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15R GLY* 5.1 2.2 - - - -
17R SER* 3.3 11.3 - - - -
18R ALA* 3.2 36.5 + - + +
21R ILE* 4.1 14.1 - - + +
1003R PO4 3.8 15.0 + - - -
807S SER* 5.6 0.2 - - - +
938S LEU* 2.9 41.4 + - + +
941S GLU* 1.3 79.1 - - + +
943S GLY* 1.3 59.8 + - - +
944S ASN 3.5 2.3 + - - +
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Residues in contact with GLY 943 (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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21R ILE* 3.8 15.5 - - - +
25R GLN* 3.5 10.0 + - - +
32R TYR* 3.3 29.6 - - - +
939S LYS 2.8 17.5 + - - -
941S GLU 3.4 0.2 - - - -
942S GLU* 1.3 79.2 - - - +
944S ASN* 1.3 61.6 + - - +
945S PRO* 4.6 1.9 - - - +
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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