Contacts of the helix formed by residues 21 - 31 (chain E) in PDB entry 1NUE
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 VAL 21 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ILE* 4.1 11.9 - - + -
29B GLU* 3.1 19.0 + - - +
35B LEU* 5.0 8.7 - - + -
38B MET* 4.5 8.3 - - + -
11E ILE* 4.0 13.6 - - + +
15E GLY 4.3 0.7 - - - +
16E VAL* 4.0 37.7 - - + -
20E LEU* 1.3 78.2 - - - +
22E GLY* 1.3 66.0 + - - +
24E ILE* 3.3 1.6 + - - +
25E ILE* 3.0 46.6 + - + +
74E VAL* 4.1 21.8 - - + -
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Residues in contact with GLY 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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22B GLY* 3.2 34.9 - - - +
25B ILE* 3.9 10.0 - - - +
26B LYS* 4.0 4.9 - - - -
29B GLU* 2.8 19.9 + - - -
21E VAL* 1.3 75.1 - - - +
23E GLU* 1.3 56.9 + - - +
25E ILE* 4.6 0.7 - - - -
26E LYS* 3.0 28.4 + - - +
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Residues in contact with GLU 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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26B LYS* 3.8 34.0 + - + +
29B GLU* 4.6 1.0 + - - -
30D GLN* 5.5 3.2 - - - +
19E GLY 5.3 1.3 - - - +
20E LEU* 3.8 21.2 - - + +
21E VAL 3.3 0.4 - - - -
22E GLY* 1.3 76.9 - - - +
24E ILE* 1.3 60.1 + - - +
26E LYS* 3.6 16.0 + - - +
27E ARG* 3.4 37.9 + - - +
108E PHE* 3.4 35.9 - - + -
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Residues in contact with ILE 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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11E ILE* 4.1 37.5 - - + -
20E LEU* 3.1 30.0 + - + +
21E VAL 3.8 2.5 - - - +
23E GLU* 1.3 74.8 - - + +
25E ILE* 1.3 67.1 + - - +
27E ARG* 3.1 17.5 + - - +
28E PHE* 3.4 23.2 - - + -
76E MET* 5.1 3.1 - - + -
104E ILE* 4.2 19.7 - - + -
108E PHE* 5.1 5.2 - - + -
116E ILE* 4.2 21.8 - - + +
117E ILE* 3.7 26.2 - - + -
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Residues in contact with ILE 25 (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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21B VAL* 4.2 8.3 - - + -
22B GLY* 3.9 9.2 - - - +
25B ILE* 4.0 16.6 - - + -
11E ILE* 4.5 5.2 - - + -
21E VAL* 3.0 38.7 + - + +
22E GLY 3.9 3.1 - - - +
24E ILE* 1.3 74.6 - - - +
26E LYS* 1.3 64.8 + - - +
28E PHE* 3.1 8.0 + - - +
29E GLU* 3.0 38.3 + - + +
35E LEU* 5.5 2.2 - - + -
38E MET* 3.9 27.1 - - + -
74E VAL* 5.0 0.4 - - + -
76E MET* 4.0 19.3 - - - -
78E TRP* 4.1 17.3 - - + -
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Residues in contact with LYS 26 (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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19B GLY 5.8 2.5 - - - +
22B GLY* 3.9 5.4 - - - -
23B GLU* 3.7 34.3 + - + +
26B LYS* 4.3 17.6 - - + +
26C LYS* 5.9 3.6 - - - +
22E GLY 3.0 19.2 + - - +
23E GLU* 3.7 20.1 + - - +
24E ILE 3.2 0.2 - - - -
25E ILE* 1.3 76.3 - - - +
27E ARG* 1.3 61.9 + - + +
29E GLU* 3.8 13.1 - - + +
30E GLN* 2.9 57.2 + - + +
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Residues in contact with ARG 27 (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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30D GLN* 6.1 0.2 - - - +
23E GLU* 3.4 28.1 + - - +
24E ILE* 3.1 10.1 + - - +
26E LYS* 1.3 79.1 - - + +
28E PHE* 1.3 60.6 + - - +
30E GLN* 3.7 16.3 + - - +
31E LYS* 3.3 21.7 + - - +
90E MET* 3.6 17.2 + - + +
102E GLY 3.2 18.8 + - - -
103E THR 3.6 14.5 + - - -
104E ILE* 3.7 22.2 - - + +
107E ASP* 2.8 31.1 + - - +
108E PHE* 3.4 30.8 - - - -
107F ASP 4.6 1.7 - - - +
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Residues in contact with PHE 28 (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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9E ILE* 4.0 36.8 - - + -
24E ILE* 3.4 24.9 - - + -
25E ILE* 3.1 2.9 + - - +
27E ARG* 1.3 76.2 - - - +
29E GLU* 1.3 65.7 + - - +
31E LYS* 3.4 11.8 + - - +
33E PHE* 3.4 38.9 + + - +
76E MET* 5.9 0.7 - - + -
78E TRP* 3.6 47.1 - + + -
83E VAL* 5.6 1.6 - - + -
87E GLY* 4.3 10.5 - - - -
90E MET* 4.0 23.6 - - + -
91E LEU* 4.2 15.5 - - + -
104E ILE* 4.0 20.4 - - + -
117E ILE* 4.5 0.4 - - + -
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Residues in contact with GLU 29 (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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16B VAL 4.5 1.7 - - - +
19B GLY* 3.1 35.3 - - - +
20B LEU 3.4 0.2 + - - -
21B VAL* 3.1 36.5 + - - +
22B GLY* 2.8 26.3 + - - -
23B GLU 4.6 0.3 + - - -
25E ILE* 3.0 18.1 + - - +
26E LYS* 3.8 11.1 - - + +
28E PHE* 1.3 76.7 - - - +
30E GLN* 1.3 64.2 + - + +
32E GLY* 3.1 14.2 + - - -
33E PHE 4.4 4.6 + - - +
78E TRP* 3.8 20.4 - - + -
18F ARG* 4.9 1.4 + - - -
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Residues in contact with GLN 30 (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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26E LYS* 2.9 54.7 + - + +
27E ARG* 3.9 18.4 + - - +
29E GLU* 1.3 78.2 - - + +
31E LYS* 1.3 59.0 + - - +
18F ARG* 3.1 21.1 + - - +
20F LEU* 5.5 2.3 - - + +
23F GLU* 5.4 4.2 - - - +
27F ARG* 6.0 0.4 - - - +
107F ASP* 3.8 9.7 + - - +
108F PHE* 3.4 44.0 - - + +
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Residues in contact with LYS 31 (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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27E ARG 3.3 16.0 + - - +
28E PHE 3.6 7.0 - - - +
29E GLU 3.2 0.6 - - - -
30E GLN* 1.3 79.0 - - - +
32E GLY* 1.3 58.0 + - - +
33E PHE* 3.5 27.8 - - + -
86E THR* 3.7 27.0 - - - +
90E MET* 4.1 11.4 - - + -
150E VAL* 5.1 0.3 - - - +
18F ARG* 4.1 0.3 + - - -
96F PRO* 4.2 11.3 + - - +
99F SER 5.5 0.4 + - - -
105F ARG 3.5 6.5 + - - -
106F GLY* 3.0 31.7 + - - +
107F ASP* 3.4 12.5 + - - +
108F PHE 3.6 11.4 - - - +
109F CYS* 2.6 30.7 + - - +
110F ILE* 3.4 18.7 - - + +
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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