Contacts of the helix formed by residues 21 - 31 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C ILE* 4.0 17.9 - - + +
15C GLY 4.4 0.4 - - - +
16C VAL* 3.9 38.4 - - + -
20C LEU* 1.3 78.1 - - - +
22C GLY* 1.3 61.2 + - - +
24C ILE* 3.3 1.7 + - - +
25C ILE* 3.0 43.9 + - + +
74C VAL* 4.0 17.0 - - + -
25F ILE* 4.2 11.4 - - + -
29F GLU* 3.0 18.3 + - - +
35F LEU* 5.0 8.1 - - + -
38F MET* 4.6 7.6 - - + -
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Residues in contact with GLY 22 (chain C).
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* 1.3 74.3 - - - +
23C GLU* 1.3 56.2 + - - +
25C ILE* 4.6 0.9 - - - -
26C LYS* 2.9 32.3 + - - +
22F GLY* 3.3 30.0 - - - -
25F ILE* 3.9 6.0 - - - +
26F LYS* 4.0 9.2 - - - -
29F GLU* 2.9 19.5 + - - -
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLN* 5.5 3.0 - - - +
19C GLY 5.3 1.5 + - - +
20C LEU* 3.5 21.4 + - + +
21C VAL 3.3 0.6 - - - -
22C GLY* 1.3 76.9 - - - +
24C ILE* 1.3 62.2 + - - +
26C LYS* 3.6 14.8 + - - +
27C ARG* 3.3 38.8 + - - +
108C PHE* 3.5 33.9 - - + -
26F LYS* 3.7 34.0 + - + +
29F GLU* 4.5 1.4 + - - -
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Residues in contact with ILE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 4.1 35.2 - - + -
20C LEU* 3.1 28.4 + - + +
21C VAL 3.8 3.1 - - - +
23C GLU* 1.3 75.9 - - + +
25C ILE* 1.3 65.7 + - - +
27C ARG* 3.1 17.1 + - - +
28C PHE* 3.3 23.8 - - + -
76C MET* 5.0 3.4 - - + -
104C ILE* 4.2 18.6 - - + -
108C PHE* 5.1 5.2 - - + -
116C ILE* 4.1 26.7 - - + +
117C ILE* 3.8 26.7 - - + -
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Residues in contact with ILE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 4.6 2.9 - - + -
21C VAL* 3.0 36.9 + - + +
22C GLY 4.0 2.7 - - - +
24C ILE* 1.3 74.6 - - - +
26C LYS* 1.3 63.9 + - - +
28C PHE* 3.1 7.0 + - - +
29C GLU* 3.0 38.2 + - - +
35C LEU* 5.5 2.9 - - + -
38C MET* 4.0 26.2 - - + -
74C VAL* 5.0 0.9 - - + -
76C MET* 4.0 19.5 - - - -
78C TRP* 4.1 18.4 - - + -
21F VAL* 4.2 8.3 - - + -
22F GLY* 3.9 10.3 - - - +
25F ILE* 4.0 16.8 - - + -
38F MET* 5.0 0.2 - - + -
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Residues in contact with LYS 26 (chain C).
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 2.9 18.5 + - - +
23C GLU* 3.6 20.5 + - - +
25C ILE* 1.3 77.9 - - - +
27C ARG* 1.3 64.2 + - + +
29C GLU* 3.7 12.7 - - + +
30C GLN* 2.9 56.1 + - + +
26E LYS* 5.9 3.4 - - - +
22F GLY* 3.9 5.3 - - - -
23F GLU* 3.5 34.4 + - + +
26F LYS* 4.2 17.6 - - + +
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Residues in contact with ARG 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLN* 5.9 0.4 - - - +
107B ASP 4.5 1.7 - - - +
23C GLU* 3.3 27.8 + - - +
24C ILE* 3.1 10.5 + - - +
26C LYS* 1.3 77.2 - - + +
28C PHE* 1.3 58.5 + - - +
30C GLN* 4.0 16.7 + - - +
31C LYS* 3.3 22.2 + - - +
90C MET* 3.7 17.3 - - + +
102C GLY 3.0 27.3 + - - -
103C THR 3.7 12.5 - - - -
104C ILE* 3.8 21.1 - - + +
107C ASP* 2.7 23.8 + - - -
108C PHE* 3.4 31.7 - - - -
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Residues in contact with PHE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C THR* 5.8 0.2 - - + -
9C ILE* 3.9 38.6 - - + -
24C ILE* 3.3 29.8 - - + -
25C ILE* 3.1 3.0 + - - +
27C ARG* 1.3 74.7 - - - +
29C GLU* 1.3 65.7 + - - +
31C LYS* 3.4 8.4 + - - +
32C GLY 3.5 0.2 + - - -
33C PHE* 3.3 41.7 + + - +
76C MET* 5.8 0.7 - - + -
78C TRP* 3.6 46.4 - + + -
83C VAL* 5.7 1.8 - - + -
87C GLY* 4.3 12.8 - - - -
90C MET* 4.1 22.0 - - + -
91C LEU* 4.4 13.9 - - + -
104C ILE* 3.9 21.1 - - + -
117C ILE* 4.5 0.9 - - + -
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Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG* 4.7 1.7 + - - -
25C ILE* 3.0 15.3 + - - +
26C LYS* 3.7 13.3 - - + +
28C PHE* 1.3 78.3 - - - +
30C GLN* 1.3 61.8 + - + +
32C GLY* 3.1 14.9 + - - -
33C PHE 4.4 4.2 + - - +
35C LEU* 6.2 0.2 - - + -
78C TRP* 3.9 18.4 - - + -
16F VAL 4.7 1.7 - - - +
19F GLY* 3.3 33.3 - - - +
20F LEU 4.2 0.2 - - - -
21F VAL* 2.9 37.5 + - - +
22F GLY* 2.8 28.6 + - - -
23F GLU 4.5 0.2 + - - -
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Residues in contact with GLN 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG* 3.0 21.2 + - - +
20B LEU* 5.2 3.4 - - + +
23B GLU* 5.3 4.5 - - - +
27B ARG* 6.0 0.2 - - - +
107B ASP* 3.8 8.9 + - - +
108B PHE* 3.4 43.3 - - + +
26C LYS* 2.9 48.7 + - + +
27C ARG* 4.0 18.2 + - - +
29C GLU* 1.3 76.0 - - - +
31C LYS* 1.3 58.8 + - - +
32C GLY 3.2 0.2 - - - -
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Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG* 3.9 1.2 + - - -
96B PRO* 4.2 10.7 + - - +
97B ALA* 5.8 0.2 - - - +
99B SER 5.3 1.0 + - - -
105B ARG 3.5 4.9 + - - -
106B GLY* 2.8 33.0 + - - +
107B ASP 3.4 12.8 - - - +
108B PHE 3.6 10.8 - - - +
109B CYS* 2.8 32.1 + - - +
110B ILE* 3.4 18.1 - - + +
27C ARG 3.3 16.3 + - - +
28C PHE* 3.6 8.5 - - - +
29C GLU 3.2 0.6 - - - -
30C GLN* 1.3 80.3 - - - +
32C GLY* 1.3 58.2 + - - +
33C PHE* 3.5 28.0 - - + -
86C THR* 3.6 27.7 - - - +
90C MET* 4.1 9.9 - - + -
150C VAL* 5.0 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