Contacts of the helix formed by residues 15 - 25 (chain R) 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 GLY 15 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13R GLY 3.4 1.8 - - - -
14R VAL* 1.3 79.8 - - - +
16R LYS* 1.3 64.8 + - - +
17R SER 3.2 2.9 - - - -
18R ALA* 3.2 13.2 + - - +
19R LEU* 3.2 27.1 + - - +
116R ASN* 3.8 11.0 + - - -
118R CYS* 4.4 2.9 - - - -
1003R PO4 2.9 12.7 + - - -
942S GLU* 4.8 3.1 - - - -
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Residues in contact with LYS 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R VAL* 3.8 25.4 - - + +
9R VAL* 3.3 33.2 - - - +
10R GLY* 3.1 12.5 + - - +
11R ALA 2.9 19.4 + - - -
14R VAL* 3.6 13.4 - - + +
15R GLY* 1.3 77.4 - - - +
17R SER* 1.3 62.3 + - - +
19R LEU* 3.4 10.7 + - - +
20R THR* 3.2 24.3 + - - -
57R ASP* 3.7 8.9 - - - +
58R THR* 4.9 2.9 - - - -
59R GLY* 4.1 11.9 - - - +
62R GLU* 2.7 31.4 + - - -
81R VAL* 4.0 6.5 - - + -
1003R PO4 2.7 25.2 + - - +
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Residues in contact with SER 17 (chain R).
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 3.2 0.2 - - - -
16R LYS* 1.3 73.1 - - - +
18R ALA* 1.3 60.6 + - - +
20R THR* 3.3 2.6 + - - -
21R ILE* 2.9 37.3 + - - +
57R ASP* 3.2 24.9 + - - -
59R GLY* 3.6 8.7 + - - -
1003R PO4 2.5 21.6 + - - -
938S LEU* 3.6 9.5 - - - +
939S LYS* 4.2 15.8 - - - +
942S GLU* 3.3 16.4 - - - -
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Residues in contact with ALA 18 (chain R).
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* 3.2 14.0 + - - +
17R SER* 1.3 78.8 - - - +
19R LEU* 1.3 57.4 + - - +
21R ILE* 3.6 9.2 - - - +
22R GLN* 2.8 37.0 + - + +
116R ASN* 5.7 0.2 - - - +
146R ALA* 3.7 19.3 - - + -
942S GLU* 3.2 22.8 + - + +
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Residues in contact with LEU 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R VAL* 5.1 2.9 - - + -
15R GLY 3.2 18.3 + - - +
16R LYS* 3.5 8.3 - - - +
17R SER 3.2 0.4 - - - -
18R ALA* 1.3 74.5 - - - +
20R THR* 1.3 64.9 + - - +
22R GLN* 3.4 2.7 + - - -
23R LEU* 3.0 24.8 + - - +
79R LEU* 5.2 6.7 - - + -
81R VAL* 4.1 34.5 - - + -
114R VAL* 4.3 11.7 - - + -
116R ASN* 4.5 3.1 - - + +
144R THR* 3.4 33.0 - - + +
146R ALA* 4.0 11.9 - - + -
152R VAL* 3.6 25.1 - - + +
155R ALA* 5.8 1.3 - - + -
156R PHE* 3.8 13.8 - - + -
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Residues in contact with THR 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R VAL* 3.9 15.2 - - - +
16R LYS 3.2 11.9 + - - -
17R SER 3.3 6.9 + - - -
19R LEU* 1.3 77.7 - - - +
21R ILE* 1.3 58.1 + - + +
23R LEU* 3.2 2.5 + - - +
24R ILE* 2.9 45.6 + - + +
39R SER 5.8 1.8 - - - +
40R TYR* 5.9 2.7 - - + -
55R ILE* 3.8 24.5 - - + +
57R ASP* 3.4 26.5 - - + +
156R PHE* 4.3 8.7 - - - -
939S LYS* 4.9 9.4 - - - +
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Residues in contact with ILE 21 (chain R).
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 2.9 31.0 + - - +
18R ALA* 3.6 5.6 - - - +
20R THR* 1.3 77.3 - - + +
22R GLN* 1.3 61.5 + - + +
24R ILE* 4.9 1.8 - - - -
25R GLN* 2.8 68.2 + - + +
32R TYR* 3.8 22.4 - - + +
939S LYS* 3.5 45.3 - - + +
942S GLU* 4.1 8.5 - - + +
943S GLY* 3.8 18.2 - - - +
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Residues in contact with GLN 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R ALA* 2.8 29.3 + - + +
19R LEU 3.8 4.0 - - - +
21R ILE* 1.3 75.0 - - + +
23R LEU* 1.3 58.7 + - - +
25R GLN* 3.6 10.0 - - - +
27R HIS* 2.6 57.4 + - - -
146R ALA 2.5 32.8 + - - +
147R LYS* 4.0 10.1 + - - +
149R ARG* 3.2 21.5 + - + +
152R VAL* 4.1 19.8 - - + +
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Residues in contact with LEU 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19R LEU 3.0 17.2 + - - +
20R THR 3.6 2.7 - - - +
21R ILE 3.1 0.2 - - - -
22R GLN* 1.3 80.2 - - - +
24R ILE* 1.3 61.7 + - + +
25R GLN 4.5 0.7 - - - +
27R HIS* 4.8 1.9 - - - -
42R LYS* 3.1 27.5 + - + +
44R VAL* 5.7 3.4 - - + -
53R LEU* 4.4 11.2 - - + -
55R ILE* 3.1 35.7 - - + -
152R VAL* 3.8 9.4 - - + +
153R GLU* 4.5 26.2 - - + -
156R PHE* 3.6 37.2 - - + -
157R TYR* 4.6 10.3 - - + +
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Residues in contact with ILE 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R THR* 2.9 25.3 + - + +
21R ILE* 4.2 2.2 - - - +
23R LEU* 1.3 80.1 - - + +
25R GLN* 1.3 70.9 + - - +
32R TYR* 6.1 3.1 - - + +
38R ASP 5.2 0.2 - - - +
39R SER* 3.3 33.0 - - - +
40R TYR 4.3 6.5 - - - +
41R ARG 4.0 17.7 - - - +
42R LYS* 3.6 41.0 + - + +
55R ILE* 3.4 31.4 - - + -
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Residues in contact with GLN 25 (chain R).
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* 2.8 45.2 + - + +
22R GLN* 3.6 15.6 - - - +
23R LEU 4.5 0.3 - - - +
24R ILE* 1.3 82.7 - - - +
26R ASN* 1.3 72.5 + - - +
27R HIS* 3.3 34.6 + - + -
32R TYR* 3.5 42.1 - - + +
42R LYS* 5.1 1.7 + - - -
943S GLY* 3.5 13.5 + - - +
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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