Contacts of the helix formed by residues 21 - 31 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C ILE* 4.2 11.0 - - + -
29C GLU* 2.9 18.1 + - - +
35C LEU* 5.1 7.4 - - + -
38C MET* 4.6 8.1 - - + -
11F ILE* 3.9 18.6 - - + +
15F GLY 4.3 0.4 - - - +
16F VAL* 3.9 38.8 - - + +
20F LEU* 1.3 77.9 - - - +
22F GLY* 1.3 63.1 + - - +
24F ILE* 3.3 1.4 + - - +
25F ILE* 3.1 43.7 + - + +
74F VAL* 4.0 16.8 - - + -
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Residues in contact with GLY 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLY* 3.3 34.5 - - - -
25C ILE* 3.9 6.0 - - - +
26C LYS* 3.9 9.6 - - - -
29C GLU* 2.8 20.6 + - - -
21F VAL* 1.3 73.6 - - - +
23F GLU* 1.3 61.7 + - - +
25F ILE* 4.7 0.7 - - - -
26F LYS* 3.0 23.0 + - - +
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Residues in contact with GLU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LYS* 3.5 35.8 + - + +
29C GLU* 4.5 1.0 + - - -
30E GLN* 5.4 3.5 - - - +
19F GLY 5.4 1.3 + - - +
20F LEU* 3.7 20.8 - - + +
21F VAL 3.3 0.2 - - - -
22F GLY* 1.3 77.5 - - - +
24F ILE* 1.3 60.4 + - - +
26F LYS* 3.6 16.8 + - - +
27F ARG* 3.4 37.0 + - - +
108F PHE* 3.4 33.9 - - + -
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Residues in contact with ILE 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ILE* 4.0 36.1 - - + -
20F LEU* 3.0 27.2 + - + +
21F VAL 3.8 3.1 - - - +
23F GLU* 1.3 74.6 - - - +
25F ILE* 1.3 66.6 + - - +
27F ARG* 3.1 17.8 + - - +
28F PHE* 3.4 23.6 - - + -
76F MET* 5.0 4.0 - - + -
104F ILE* 4.2 18.6 - - + -
108F PHE* 5.0 6.3 - - + -
116F ILE* 4.1 25.8 - - + +
117F ILE* 3.8 25.1 - - + -
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Residues in contact with ILE 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 4.2 8.1 - - + -
22C GLY* 3.9 10.1 - - - +
25C ILE* 4.0 16.4 - - + -
11F ILE* 4.6 3.6 - - + -
21F VAL* 3.1 34.7 + - + +
22F GLY 4.0 2.9 - - - +
24F ILE* 1.3 74.8 - - - +
26F LYS* 1.3 64.7 + - - +
28F PHE* 3.0 7.4 + - - +
29F GLU* 3.0 35.6 + - - +
35F LEU* 5.4 2.7 - - + -
38F MET* 3.8 28.0 - - + -
74F VAL* 5.0 0.7 - - + -
76F MET* 3.9 19.1 - - - -
78F TRP* 4.0 21.8 - - + -
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Residues in contact with LYS 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 6.0 2.4 - - - +
22C GLY* 4.0 7.4 - - - -
23C GLU* 3.7 31.4 + - + +
26C LYS* 4.2 18.2 - - + +
22F GLY 3.0 19.3 + - - +
23F GLU* 3.7 20.4 + - - +
25F ILE* 1.3 77.4 - - - +
27F ARG* 1.3 57.1 + - + +
29F GLU* 3.7 13.7 + - + +
30F GLN* 2.9 62.8 + - + +
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Residues in contact with ARG 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASP 4.5 2.1 - - - +
30E GLN* 6.0 0.2 - - - +
23F GLU* 3.4 28.1 + - - +
24F ILE* 3.1 10.5 + - - +
26F LYS* 1.3 78.9 - - + +
28F PHE* 1.3 60.3 + - + +
30F GLN* 4.0 16.2 + - - +
31F LYS* 3.4 21.3 + - - +
90F MET* 3.6 16.9 + - + +
102F GLY 3.1 26.5 + - - -
103F THR 3.6 12.7 + - - -
104F ILE* 3.8 20.4 - - + +
107F ASP* 2.8 23.8 + - - +
108F PHE* 3.4 33.8 - - - -
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Residues in contact with PHE 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 4.1 34.5 - - + -
24F ILE* 3.4 24.0 - - + -
25F ILE* 3.0 3.1 + - - +
27F ARG* 1.3 75.2 - - - +
29F GLU* 1.3 65.6 + - - +
31F LYS* 3.4 8.2 + - - +
32F GLY 3.5 0.2 + - - -
33F PHE* 3.3 39.0 + + - +
76F MET* 5.9 0.7 - - + -
78F TRP* 3.6 45.5 - + + -
83F VAL* 5.6 2.5 - - + -
87F GLY* 4.3 12.1 - - - -
90F MET* 3.9 27.4 - - + -
91F LEU* 4.3 15.7 - - + -
104F ILE* 3.8 21.1 - - + -
117F ILE* 4.6 0.4 - - + -
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Residues in contact with GLU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL 4.6 1.6 - - - +
19C GLY* 3.2 35.6 - - - +
21C VAL* 3.0 34.1 + - - +
22C GLY* 2.9 29.0 + - - -
23C GLU 4.5 0.3 + - - -
18D ARG* 4.7 1.4 + - - -
25F ILE* 3.0 14.5 + - - +
26F LYS* 3.3 13.8 + - + +
28F PHE* 1.3 76.6 - - - +
30F GLN* 1.3 62.8 + - + +
32F GLY* 3.1 15.1 + - - -
33F PHE 4.3 4.0 + - - +
35F LEU* 6.2 0.2 - - + -
78F TRP* 3.8 19.7 - - + -
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Residues in contact with GLN 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ARG* 3.1 19.0 + - - +
20D LEU* 5.3 2.8 - - + +
23D GLU* 5.4 4.0 - - - +
27D ARG* 5.9 0.6 - - - +
107D ASP* 3.8 9.3 + - - +
108D PHE* 3.4 46.3 - - + -
26F LYS* 2.9 55.3 + - + +
27F ARG* 4.0 16.8 + - - +
29F GLU* 1.3 73.7 - - + +
31F LYS* 1.3 59.9 + - - +
32F GLY 3.2 0.2 - - - -
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Residues in contact with LYS 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ARG* 3.8 2.0 + - - -
96D PRO* 4.3 9.9 + - - +
99D SER 5.5 0.6 + - - -
105D ARG 3.5 4.8 + - - -
106D GLY* 2.8 32.8 + - - +
107D ASP* 3.3 12.1 + - - +
108D PHE 3.5 10.9 - - - +
109D CYS* 2.8 29.2 + - - +
110D ILE* 3.4 20.6 - - + +
27F ARG 3.4 15.5 + - - +
28F PHE 3.6 6.5 - - - +
29F GLU 3.2 0.4 - - - -
30F GLN* 1.3 81.0 - - - +
32F GLY* 1.3 57.2 + - - +
33F PHE* 3.4 26.2 - - + -
86F THR* 3.7 27.7 - - - +
90F MET* 4.2 12.5 - - + +
150F VAL* 5.1 0.2 - - - +
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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