Contacts of the helix formed by residues 21 - 31 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.9 18.6 - - + +
15B GLY 4.4 0.7 - - - +
16B VAL* 4.0 37.9 - - + +
20B LEU* 1.3 77.2 - - - +
22B GLY* 1.3 62.6 + - - +
24B ILE* 3.9 1.6 - - - +
25B ILE* 3.1 47.3 + - + +
74B VAL* 4.1 16.8 - - + -
25E ILE* 4.2 11.0 - - + -
29E GLU* 3.1 19.2 + - - +
35E LEU* 5.1 7.6 - - + -
38E MET* 4.5 8.1 - - + -
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Residues in contact with GLY 22 (chain B).
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* 1.3 73.2 - - - +
23B GLU* 1.3 61.8 + - - +
25B ILE* 3.4 1.1 + - - -
26B LYS* 2.9 26.4 + - - +
22E GLY* 3.2 32.0 - - - -
25E ILE* 3.9 6.0 - - - +
26E LYS* 3.9 7.6 - - - -
29E GLU* 2.8 18.8 + - - -
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Residues in contact with GLU 23 (chain B).
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 5.3 1.5 + - - +
20B LEU* 3.5 20.8 + - + +
21B VAL 3.3 0.2 - - - -
22B GLY* 1.3 76.9 - - - +
24B ILE* 1.3 62.0 + - - +
26B LYS* 3.5 17.0 + - - +
27B ARG* 3.4 36.1 + - - +
108B PHE* 3.4 34.5 - - + -
30C GLN* 5.3 4.7 - - - +
26E LYS* 3.7 35.5 + - + +
29E GLU* 4.6 0.6 + - - -
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 4.0 37.2 - - + -
15B GLY* 5.3 0.2 - - - -
20B LEU* 3.0 27.6 + - + +
21B VAL 3.9 2.9 - - - +
23B GLU* 1.3 72.6 - - - +
25B ILE* 1.3 67.1 + - - +
27B ARG* 3.2 17.3 + - - +
28B PHE* 3.4 24.4 - - + -
76B MET* 5.0 3.8 - - + -
104B ILE* 4.2 17.5 - - + -
108B PHE* 4.9 7.4 - - + -
116B ILE* 4.2 24.9 - - + +
117B ILE* 3.8 26.5 - - + -
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 4.7 3.6 - - + -
21B VAL* 3.1 34.9 + - + +
22B GLY 3.8 2.9 - - - +
24B ILE* 1.3 75.3 - - - +
26B LYS* 1.3 63.3 + - - +
28B PHE* 3.0 7.7 + - - +
29B GLU* 3.0 36.2 + - - +
35B LEU* 5.6 1.8 - - + -
38B MET* 3.9 26.0 - - - -
74B VAL* 5.0 1.1 - - + -
76B MET* 4.0 19.1 - - + -
78B TRP* 4.0 18.3 - - + -
21E VAL* 4.1 9.9 - - + -
22E GLY* 3.9 10.1 - - - +
25E ILE* 4.0 16.2 - - + -
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Residues in contact with LYS 26 (chain B).
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 2.9 17.6 + - - +
23B GLU* 3.5 21.0 + - - +
25B ILE* 1.3 77.7 - - - +
27B ARG* 1.3 56.6 + - + +
29B GLU* 3.8 13.0 - - + +
30B GLN* 2.9 62.5 + - + +
26D LYS* 5.8 4.2 - - - +
19E GLY 5.9 2.0 - - - +
22E GLY* 4.0 5.8 - - - -
23E GLU* 3.8 31.6 + - + +
26E LYS* 4.3 17.8 - - + +
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Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASP 4.6 1.4 - - - +
23B GLU* 3.5 27.3 + - - +
24B ILE* 3.2 9.5 + - - +
25B ILE 3.2 1.2 - - - -
26B LYS* 1.3 78.1 - - + +
28B PHE* 1.3 60.5 + - + +
30B GLN* 3.9 16.3 + - - +
31B LYS* 3.4 23.0 + - - +
90B MET* 3.6 16.1 - - + +
102B GLY 3.2 19.2 + - - -
103B THR 3.7 12.5 - - - -
104B ILE* 3.8 20.9 - - + +
107B ASP* 2.8 30.7 + - - +
108B PHE* 3.4 30.9 - - - -
30C GLN* 6.0 0.4 - - - +
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Residues in contact with PHE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 4.0 32.5 - - + -
24B ILE* 3.4 30.5 - - + -
25B ILE* 3.0 3.1 + - - +
27B ARG* 1.3 75.8 - - - +
29B GLU* 1.3 66.2 + - - +
31B LYS* 3.5 6.3 + - - +
32B GLY 3.6 0.2 + - - -
33B PHE* 3.3 40.3 + + - +
76B MET* 5.8 0.9 - - + -
78B TRP* 3.7 46.9 - + + -
83B VAL* 5.7 1.8 - - + -
87B GLY* 4.3 11.4 - - - -
90B MET* 3.9 23.1 - - + -
91B LEU* 4.3 15.7 - - + -
104B ILE* 4.0 22.2 - - + -
117B ILE* 4.5 4.0 - - + -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 4.9 1.2 + - - -
25B ILE* 3.0 15.9 + - - +
26B LYS* 3.8 11.3 - - + +
28B PHE* 1.3 78.4 - - - +
30B GLN* 1.3 61.8 + - + +
32B GLY* 3.1 14.7 + - - -
33B PHE 4.4 4.9 + - - +
78B TRP* 3.9 20.0 - - + -
16E VAL 4.5 1.9 - - - +
19E GLY* 3.1 36.4 - - - +
20E LEU 3.4 0.2 + - - -
21E VAL* 3.1 35.1 + - - +
22E GLY* 2.8 28.1 + - - -
23E GLU 4.6 0.5 + - - -
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Residues in contact with GLN 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.0 20.8 + - - +
20A LEU* 5.4 2.6 - - + +
23A GLU* 5.5 3.3 - - - +
27A ARG* 6.0 0.4 - - - +
107A ASP* 3.8 9.5 + - - +
108A PHE* 3.6 44.4 - - + +
26B LYS* 2.9 52.2 + - + +
27B ARG* 3.9 18.5 + - - +
29B GLU* 1.3 77.2 - - + +
31B LYS* 1.3 57.7 + - - +
32B GLY 3.2 0.2 - - - -
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.9 1.6 + - - -
96A PRO* 4.2 10.3 + - - +
99A SER 5.4 1.0 + - - -
105A ARG 3.5 5.1 + - - -
106A GLY* 2.9 32.0 + - - +
107A ASP 3.4 13.2 + - - +
108A PHE 3.5 12.0 - - - +
109A CYS* 2.7 29.3 + - - +
110A ILE* 3.4 18.1 - - + +
27B ARG 3.4 15.3 + - - +
28B PHE 3.7 7.2 - - - +
29B GLU 3.2 0.2 - - - -
30B GLN* 1.3 79.2 - - - +
32B GLY* 1.3 57.6 + - - +
33B PHE* 3.5 27.8 - - + -
86B THR* 3.7 28.8 - - - +
90B MET* 4.1 12.1 - - + -
150B 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