Contacts of the helix formed by residues 14 - 24 (chain E) in PDB entry 1NVI
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 SER 14 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E PHE* 1.3 75.9 - - - +
15E VAL* 1.3 63.9 + - - +
16E GLY* 3.3 6.6 + - - -
17E GLU* 3.0 50.3 + - - +
18E GLU* 3.0 18.2 + - - +
93E GLU* 5.1 1.1 - - - -
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Residues in contact with VAL 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E PHE* 4.3 4.3 - - + -
14E SER* 1.3 71.4 + - - +
16E GLY* 1.3 57.4 + - - +
18E GLU* 4.4 6.5 - - - +
19E TYR* 2.8 41.3 + - + +
33E THR* 4.8 10.1 - - + +
35E THR* 3.5 24.9 - - + +
93E GLU* 4.3 16.4 + - - +
96E PHE* 3.9 25.1 - - + -
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Residues in contact with GLY 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E SER* 3.1 7.8 + - - -
15E VAL* 1.3 79.8 - - - +
17E GLU* 1.3 56.1 + - - +
19E TYR* 4.8 2.4 - - - +
20E PRO* 3.1 24.0 - - - +
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Residues in contact with GLU 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E PHE* 5.6 1.0 - - - -
14E SER* 3.0 30.9 + - - +
16E GLY* 1.3 77.1 - - - +
18E GLU* 1.3 71.6 + - - +
20E PRO* 3.5 10.0 - - - +
21E TRP* 4.8 4.3 + - - +
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Residues in contact with GLU 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LYS* 2.6 39.9 + - - +
13E PHE* 4.6 9.4 - - + +
14E SER 3.0 20.4 + - - +
15E VAL* 3.9 3.6 - - - +
17E GLU* 1.3 87.3 - - - +
19E TYR* 1.3 65.8 + - - +
20E PRO 3.5 0.4 - - - -
21E TRP* 3.7 10.6 + - - +
22E LEU* 3.5 17.7 + - - +
80E THR* 4.1 5.6 + - + +
82E ILE* 3.5 30.0 - - + +
96E PHE* 3.9 25.3 - - + -
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Residues in contact with TYR 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E VAL* 2.8 26.3 + - + +
16E GLY* 4.8 2.2 - - - +
18E GLU* 1.3 76.8 - - - +
20E PRO* 1.3 76.3 - - + +
22E LEU* 3.1 10.8 + - + +
23E ALA* 2.9 42.7 + - + +
31E VAL* 3.5 35.6 - - + +
33E THR* 4.4 14.4 - - + -
96E PHE* 5.1 2.0 - - - -
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Residues in contact with PRO 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLY 3.1 24.5 - - - +
17E GLU* 3.5 12.1 - - - +
19E TYR* 1.3 101.1 - - + +
21E TRP* 1.3 60.0 + - - +
23E ALA* 3.2 3.8 + - + +
24E GLU* 3.1 27.7 + - - +
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Residues in contact with TRP 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E GLU* 3.7 48.9 + - + -
4E THR 4.5 0.2 - - - -
5E LYS* 4.2 24.7 - - + +
17E GLU 4.8 3.9 + - - +
18E GLU* 3.7 12.2 + - - +
19E TYR 3.3 0.6 - - - -
20E PRO* 1.3 78.1 - - - +
22E LEU* 1.3 75.5 + - + +
23E ALA 3.4 0.3 + - - -
24E GLU* 3.4 20.9 + - - +
78E ARG* 2.8 75.7 + - + +
79E VAL 3.9 9.2 - - - -
80E THR* 3.3 26.9 - - - -
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Residues in contact with LEU 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E GLU 3.5 8.5 + - - +
19E TYR* 3.1 11.2 + - - +
21E TRP* 1.3 83.5 - - + +
23E ALA* 1.3 60.3 + - - +
24E GLU 3.3 1.1 + - - -
25E ARG 4.6 2.3 + - - -
28E ASP* 4.8 3.5 - - - +
31E VAL* 4.0 19.7 - - + -
33E THR* 4.2 11.0 - - + -
78E ARG* 3.7 40.8 - - + +
80E THR* 3.6 21.1 - - - +
96E PHE* 4.3 11.0 - - + -
98E GLY* 3.5 35.0 - - - +
100E THR* 3.3 30.4 - - + +
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TYR* 2.9 51.2 + - + +
20E PRO* 3.7 3.8 - - + +
21E TRP 3.2 0.4 - - - -
22E LEU* 1.3 74.7 - - - +
24E GLU* 1.3 64.3 + - - +
25E ARG 3.4 10.8 + - - +
26E ASP* 5.6 0.3 - - - +
28E ASP* 5.6 1.1 - - - +
31E VAL* 4.2 12.8 - - + -
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Residues in contact with GLU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E PRO* 3.1 10.4 + - - +
21E TRP* 3.5 23.1 + - - +
22E LEU 3.3 2.2 - - - -
23E ALA* 1.3 78.1 - - - +
25E ARG* 1.3 61.7 + - + +
26E ASP* 3.5 11.1 + - - +
78E ARG* 2.9 39.4 + - - +
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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