Contacts of the helix formed by residues 15 - 26 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13Q GLY 3.4 0.4 - - - -
14Q VAL* 1.3 80.3 - - - +
16Q LYS* 1.3 67.0 + - - +
17Q SER 3.3 2.9 - - - -
18Q ALA* 3.9 0.2 - - - +
19Q LEU* 2.9 32.4 + - - +
81Q VAL* 5.0 0.2 - - - -
116Q ASN* 3.6 10.8 - - - -
1001Q GTP 3.0 31.3 + - - -
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Residues in contact with LYS 16 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q VAL* 3.6 27.0 - - + +
9Q VAL* 3.3 37.7 - - - +
10Q GLY 3.0 11.4 + - - +
11Q ALA 2.9 20.2 + - - -
14Q VAL* 3.8 11.2 - - + +
15Q GLY* 1.3 77.4 - - - +
17Q SER* 1.3 60.7 + - - +
19Q LEU* 3.7 6.0 - - - +
20Q THR* 2.9 28.1 + - - -
57Q ASP* 3.6 12.3 - - - +
58Q THR* 3.1 26.0 - - - -
60Q GLY* 3.8 3.8 - - - +
81Q VAL* 4.3 2.5 - - + -
1001Q GTP 2.7 48.0 + - - +
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Residues in contact with SER 17 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Q LYS* 1.3 73.0 - - - +
18Q ALA* 1.3 60.2 + - - +
20Q THR* 3.2 3.0 + - - -
21Q ILE* 2.9 46.9 + - - +
29Q VAL* 6.3 1.6 - - - -
33Q ASP 5.6 1.3 - - - -
35Q THR* 2.8 4.5 + - - -
38Q ASP* 5.3 0.3 + - - -
40Q TYR* 5.7 0.7 - - - -
57Q ASP* 2.6 24.4 + - - -
1001Q GTP 3.1 15.1 + - - -
1002Q MG 2.4 28.8 - - - -
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Residues in contact with ALA 18 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Q GLY 3.9 0.9 - - - +
17Q SER* 1.3 76.4 - - - +
19Q LEU* 1.3 57.6 + - - +
21Q ILE* 4.1 4.3 - - - +
22Q GLN* 2.9 31.5 + - - +
27Q HIS 4.5 1.7 - - - +
28Q PHE* 4.1 13.0 - - + -
29Q VAL* 4.5 16.4 - - + +
146Q ALA* 3.5 12.8 - - + +
1001Q GTP 2.9 44.9 + - + +
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Residues in contact with LEU 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q VAL* 5.5 0.9 - - + -
15Q GLY 2.9 23.6 + - - +
16Q LYS* 3.7 4.3 - - - +
18Q ALA* 1.3 78.0 - - - +
20Q THR* 1.3 62.6 - - - +
22Q GLN* 3.6 3.3 - - - +
23Q LEU* 3.1 22.2 + - - +
79Q LEU* 5.3 6.5 - - + -
81Q VAL* 4.0 27.4 - - + -
114Q VAL* 4.1 12.6 - - + -
116Q ASN* 3.4 33.9 - - - +
144Q THR* 3.4 12.3 - - + +
146Q ALA* 3.6 8.0 - - + +
152Q VAL* 3.8 31.7 - - + +
156Q PHE* 3.9 13.4 - - + -
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Residues in contact with THR 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q VAL* 3.9 11.8 - - - +
16Q LYS 2.9 17.9 + - - -
17Q SER* 3.6 6.3 - - - -
19Q LEU* 1.3 77.9 - - - +
21Q ILE* 1.3 58.3 + - - +
23Q LEU* 3.2 2.9 + - - +
24Q ILE* 2.9 38.0 + - + +
40Q TYR* 3.6 39.5 - - + -
55Q ILE* 3.8 21.2 - - + +
57Q ASP* 4.4 6.5 - - + +
156Q PHE* 3.9 17.3 - - - -
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Residues in contact with ILE 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q SER* 2.9 33.0 + - - +
18Q ALA 4.1 2.2 - - - +
20Q THR* 1.3 68.8 - - - +
22Q GLN* 1.3 60.4 + - - +
24Q ILE* 4.4 6.3 - - - +
25Q GLN* 2.8 48.6 + - - +
26Q ASN 3.5 2.9 + - - -
27Q HIS* 3.6 20.7 - - + +
29Q VAL* 3.6 31.9 - - + -
40Q TYR* 3.8 31.4 - - + +
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Residues in contact with GLN 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q ALA 2.9 19.5 + - - +
19Q LEU* 3.6 5.4 - - - +
21Q ILE* 1.3 76.7 - - - +
23Q LEU* 1.3 58.8 + - - +
26Q ASN* 2.9 36.0 + - - +
27Q HIS 3.4 23.5 + - - +
28Q PHE* 3.8 7.7 - - - +
146Q ALA* 2.7 32.3 + - - +
147Q LYS 3.9 4.4 + - - -
149Q ARG* 2.8 65.6 + - + +
152Q VAL* 4.2 10.5 - - + -
753S THR* 3.9 12.5 + - - -
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Residues in contact with LEU 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q LEU 3.1 13.2 + - - +
20Q THR 3.2 7.4 + - - +
22Q GLN* 1.3 80.4 - - - +
24Q ILE* 1.3 57.5 - - + +
26Q ASN* 4.3 6.2 - - - +
42Q LYS* 3.2 36.2 + - + -
53Q LEU* 4.8 4.0 - - + -
55Q ILE* 3.5 27.1 - - + -
149Q ARG* 4.4 6.8 + - - +
152Q VAL* 4.2 6.7 - - + +
153Q GLU* 4.2 20.4 - - + -
156Q PHE* 3.5 41.1 - - + -
157Q TYR* 3.9 28.0 - - + +
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Residues in contact with ILE 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Q THR* 2.9 26.6 + - + +
21Q ILE* 4.1 4.0 - - - +
23Q LEU* 1.3 80.7 - - + +
25Q GLN* 1.3 65.1 + - + +
26Q ASN* 4.7 1.7 - - - +
40Q TYR* 4.0 39.5 - - + -
41Q ARG 4.1 3.8 - - - +
42Q LYS* 3.7 36.6 + - + +
55Q ILE* 4.2 13.0 - - + -
976S ASN* 3.3 48.6 - - + +
977S GLN* 4.1 9.4 + - - +
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Residues in contact with GLN 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q ILE* 2.8 33.3 + - + +
24Q ILE* 1.3 90.2 - - + +
26Q ASN* 1.3 72.1 + - - +
27Q HIS* 3.1 9.3 + - + -
40Q TYR* 6.0 4.5 - - - -
750S HIS* 4.1 20.7 + - + +
752S ILE* 3.7 13.2 - - - +
797S ARG* 5.8 0.5 + - - -
976S ASN* 3.1 35.4 + - + +
978S PRO* 3.8 7.2 - - - +
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Residues in contact with ASN 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q GLN* 2.9 28.6 + - - +
23Q LEU 4.3 6.8 - - - +
24Q ILE 4.7 1.6 - - - +
25Q GLN* 1.3 81.7 - - - +
27Q HIS* 1.3 55.2 + - - +
42Q LYS* 5.5 1.7 + - - -
149Q ARG* 3.4 29.9 + - - +
752S ILE* 3.4 8.6 - - + -
753S THR* 3.0 44.5 + - - +
754S PHE* 3.9 16.1 - - - +
755S GLN* 4.8 1.8 - - - +
977S GLN* 5.2 2.9 - - - +
978S PRO* 4.0 23.1 - - + +
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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