Contacts of the helix formed by residues 21 - 31 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.9 17.6 - - + +
15A GLY 4.0 0.6 + - - +
16A VAL* 4.0 31.4 - - + +
20A LEU* 1.3 76.7 - - - +
22A GLY* 1.3 65.0 + - - +
24A ILE* 3.3 1.6 + - - +
25A ILE* 3.0 47.1 + - + +
74A VAL* 4.1 25.1 - - + -
25D ILE* 4.1 11.2 - - + -
29D GLU* 3.0 17.2 + - - +
35D LEU* 5.0 7.9 - - + -
38D MET* 4.5 8.1 - - + -
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Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 1.3 75.5 - - - +
23A GLU* 1.3 62.0 + - - +
25A ILE* 4.6 1.1 - - - -
26A LYS* 3.0 26.0 + - - +
22D GLY* 3.3 30.2 - - - -
25D ILE* 3.8 10.9 - - - +
26D LYS* 4.0 4.3 - - - -
29D GLU* 2.8 19.7 + - - -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY 5.4 1.3 + - - +
20A LEU* 3.4 19.9 + - + +
21A VAL 3.3 0.6 - - - -
22A GLY* 1.3 77.2 - - - +
24A ILE* 1.3 61.1 + - - +
26A LYS* 3.5 16.1 + - - +
27A ARG* 3.4 38.7 + - - +
108A PHE* 3.4 34.3 - - + -
30B GLN* 5.5 3.2 - - - +
26D LYS* 3.7 35.2 + - + +
29D GLU* 4.5 1.0 + - - -
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.1 34.8 - - + -
20A LEU* 3.0 33.9 + - + +
21A VAL 3.8 3.1 - - - +
23A GLU* 1.3 73.0 - - - +
25A ILE* 1.3 68.2 + - - +
27A ARG* 3.1 17.2 + - - +
28A PHE* 3.4 24.0 - - + -
76A MET* 5.0 4.3 - - + -
104A ILE* 4.2 20.2 - - + -
108A PHE* 5.0 6.7 - - + -
116A ILE* 4.3 22.0 - - + +
117A ILE* 3.8 26.2 - - + -
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.6 3.4 - - + -
21A VAL* 3.0 39.9 + - + +
22A GLY 3.9 3.1 - - - +
24A ILE* 1.3 77.3 - - - +
26A LYS* 1.3 63.0 + - - +
28A PHE* 3.1 6.4 + - - +
29A GLU* 3.0 38.5 + - + +
35A LEU* 5.6 2.2 - - + -
38A MET* 3.9 26.7 - - + -
74A VAL* 5.1 0.4 - - + -
76A MET* 3.9 20.9 - - + -
78A TRP* 3.9 17.7 - - + -
21D VAL* 4.1 7.4 - - + -
22D GLY* 3.9 10.3 - - - +
25D ILE* 4.0 16.4 - - + -
38D MET* 4.9 0.2 - - + -
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY 3.0 19.1 + - - +
23A GLU* 3.6 20.5 + - - +
24A ILE 3.2 0.2 - - - -
25A ILE* 1.3 77.9 - - - +
27A ARG* 1.3 57.3 + - + +
29A GLU* 3.7 13.4 - - + +
30A GLN* 3.0 61.5 + - + +
19D GLY 5.9 1.6 - - - +
22D GLY* 4.2 5.6 - - - -
23D GLU* 3.7 34.2 + - + +
26D LYS* 4.1 19.0 - - + +
26F LYS* 6.0 2.2 - - - +
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 3.4 28.4 + - - +
24A ILE* 3.1 10.8 + - - +
26A LYS* 1.3 78.3 - - + +
28A PHE* 1.3 60.6 + - - +
30A GLN* 4.0 16.3 + - - +
31A LYS* 3.4 21.1 + - - +
90A MET* 3.5 18.6 + - + +
102A GLY 3.1 26.7 + - - -
103A THR 3.6 13.5 + - - -
104A ILE* 3.8 20.8 - - + +
107A ASP* 2.8 23.2 + - - -
108A PHE* 3.5 30.1 - - - -
30B GLN* 6.0 0.4 - - - +
107C ASP 4.6 2.1 - - - +
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.1 33.4 - - + -
24A ILE* 3.4 23.8 - - + -
25A ILE* 3.1 3.3 + - - +
27A ARG* 1.3 76.1 - - - +
29A GLU* 1.3 63.8 + - - +
31A LYS* 3.4 8.3 + - - +
32A GLY 3.4 0.3 + - - -
33A PHE* 3.3 40.7 + + - +
76A MET* 5.8 0.7 - - + -
78A TRP* 3.6 46.4 - + + -
83A VAL* 5.5 2.7 - - + -
87A GLY* 4.3 14.4 - - - -
90A MET* 4.0 24.7 - - + -
91A LEU* 4.3 14.8 - - + -
104A ILE* 3.9 21.1 - - + -
117A ILE* 4.5 0.4 - - + -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.0 15.3 + - + +
26A LYS* 3.4 12.8 + - + +
28A PHE* 1.3 77.3 - - - +
30A GLN* 1.3 62.1 + - - +
32A GLY* 3.1 14.4 + - - -
33A PHE 4.5 4.3 - - - +
35A LEU* 6.2 0.2 - - + -
78A TRP* 3.9 18.8 - - + -
18C ARG* 4.8 1.4 + - - -
16D VAL 4.7 1.9 - - - +
19D GLY* 3.3 33.1 - - - +
21D VAL* 3.0 35.4 + - - +
22D GLY* 2.8 29.5 + - - -
23D GLU 4.6 0.3 + - - -
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Residues in contact with GLN 30 (chain A).
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* 3.0 52.2 + - + +
27A ARG* 4.0 16.8 + - - +
29A GLU* 1.3 77.3 - - + +
31A LYS* 1.3 59.1 + - - +
18C ARG* 3.0 22.7 + - - +
20C LEU* 5.5 2.1 - - + +
23C GLU* 5.5 3.1 - - - +
27C ARG* 5.9 0.4 - - - +
107C ASP* 3.8 10.5 + - - +
108C PHE* 3.5 44.5 - - + +
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG 3.4 16.0 + - - +
28A PHE 3.4 6.9 + - - +
29A GLU 3.2 0.4 - - - -
30A GLN* 1.3 79.2 - - - +
32A GLY* 1.3 58.1 + - - +
33A PHE* 3.5 27.8 - - + -
86A THR* 3.7 27.1 - - - +
90A MET* 4.2 11.4 - - + -
150A VAL* 5.0 0.7 - - - +
18C ARG* 4.1 1.6 + - - -
96C PRO* 4.2 10.7 + - - +
97C ALA* 5.8 0.4 - - - +
99C SER 5.2 1.0 + - - -
105C ARG 3.6 5.1 + - - -
106C GLY* 2.9 33.0 + - - +
107C ASP* 3.4 13.2 + - - +
108C PHE 3.6 11.4 - - - +
109C CYS* 2.8 29.8 + - - +
110C 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