Contacts of the helix formed by residues 23 - 36 (chain A) in PDB entry 2NMU
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 GLU 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 5.4 0.2 - - - -
21A GLY 3.7 1.8 + - - +
22A GLN* 1.3 73.5 - - - +
24A VAL* 1.3 64.8 + - - +
25A PHE* 3.0 23.3 + - - +
26A SER* 2.7 58.4 + - - +
27A GLN* 3.2 12.7 + - - +
103A PRO* 3.5 3.8 - - - +
104A GLY* 2.8 37.3 + - - +
105A CYS 3.2 14.6 + - - +
106A THR* 4.4 8.5 - - + +
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Residues in contact with VAL 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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18A LEU* 4.3 7.9 - - + -
23A GLU* 1.3 69.1 - - - +
25A PHE* 1.3 61.5 + - + +
27A GLN* 3.3 1.9 + - - +
28A LEU* 2.9 49.5 + - + +
49A LEU* 4.0 19.5 - - + -
74A LEU* 4.6 2.9 - - + -
101A MSE 4.1 24.2 - - + -
105A CYS* 2.9 23.1 + - + +
107A VAL* 4.3 9.4 - - + -
111A LEU* 3.9 31.4 - - + -
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Residues in contact with PHE 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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23A GLU* 3.0 19.8 + - - +
24A VAL* 1.3 76.2 - - + +
26A SER* 1.3 63.7 + - - +
28A LEU* 3.8 5.1 - - + +
29A HIS* 3.0 51.8 + + + +
83A GLU* 3.9 32.1 - - + -
85A LEU* 4.3 17.5 - - + -
100A HIS* 6.2 0.4 - + - -
101A MSE 3.2 57.0 - - + -
102A MSE 3.8 11.2 - - - -
103A PRO* 3.6 30.1 - - + -
105A CYS* 6.1 0.2 - - + -
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Residues in contact with SER 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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23A GLU* 2.7 46.8 + - - +
25A PHE* 1.3 73.3 - - - +
27A GLN* 1.3 63.9 + - - +
29A HIS* 3.4 10.3 + - - +
30A ALA* 2.9 27.4 + - - +
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Residues in contact with GLN 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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16A LEU* 5.5 1.0 - - - +
18A LEU* 3.8 26.5 - - + +
22A GLN* 3.6 46.1 + - + +
23A GLU 3.2 16.8 + - - +
24A VAL 3.3 2.9 + - - +
26A SER* 1.3 82.9 + - - +
28A LEU* 1.3 66.6 + - - +
30A ALA* 3.3 12.2 + - - +
31A PHE* 3.0 23.4 + - - +
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Residues in contact with LEU 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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16A LEU* 5.3 3.6 - - + -
18A LEU* 5.3 1.8 - - + -
24A VAL* 2.9 38.0 + - + +
25A PHE* 3.8 6.7 - - + +
27A GLN* 1.3 76.8 - - - +
29A HIS* 1.3 60.8 + - + +
31A PHE* 3.2 6.0 + - + +
32A VAL* 2.9 33.4 + - - +
42A ILE* 4.7 7.2 - - + -
74A LEU* 5.0 5.4 - - + -
78A LEU* 4.2 15.4 - - + +
85A LEU* 3.7 30.5 - - + -
113A LEU* 3.9 30.7 - - + -
115A ILE* 4.0 20.4 - - + -
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Residues in contact with HIS 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 PHE* 3.0 46.8 + + + +
26A SER* 3.7 8.1 - - - +
27A GLN 3.2 0.2 - - - -
28A LEU* 1.3 80.4 - - + +
30A ALA* 1.3 57.6 + - - +
32A VAL* 3.3 10.4 + - - +
33A GLN* 2.8 36.9 + - + +
78A LEU* 6.1 2.2 - - + +
79A GLU 5.5 4.6 + - - -
80A LEU 5.9 0.6 + - - -
82A GLY 5.4 0.2 - - - -
83A GLU* 3.0 39.6 + - + -
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Residues in contact with ALA 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 SER 2.9 17.8 + - - +
27A GLN* 3.3 17.5 + - - +
29A HIS* 1.3 75.2 - - - +
31A PHE* 1.3 58.8 + - - +
33A GLN* 3.4 6.7 + - - +
34A GLN* 2.9 33.2 + - - +
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Residues in contact with PHE 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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14A TYR* 3.4 49.4 - + + -
15A ALA 5.3 2.0 - - - -
16A LEU* 3.8 39.0 - - + -
27A GLN 3.0 14.2 + - - +
28A LEU* 3.5 10.1 - - - +
30A ALA* 1.3 75.2 - - - +
32A VAL* 1.3 65.1 + - + +
34A GLN* 3.4 12.5 + - - +
35A ASN* 3.1 45.1 + - - +
37A LEU* 4.1 17.5 - - + -
115A ILE* 4.1 16.6 - - + -
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Residues in contact with VAL 32 (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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28A LEU 2.9 21.4 + - - +
29A HIS* 3.6 10.1 - - - +
31A PHE* 1.3 78.9 - - + +
33A GLN* 1.3 58.5 + - - +
36A GLN* 2.8 25.3 + - - -
37A LEU* 3.0 35.6 + - + +
78A LEU* 3.6 32.8 - - + -
79A GLU 3.5 9.9 - - - +
80A LEU* 3.5 39.0 - - + +
115A ILE* 6.3 0.7 - - + -
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Residues in contact with GLN 33 (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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29A HIS* 2.8 23.4 + - + +
30A ALA* 3.7 6.7 - - - +
32A VAL* 1.3 76.4 - - - +
34A GLN* 1.3 66.3 + - - +
36A GLN* 2.7 37.7 + - - +
80A LEU* 3.1 43.5 + - - +
81A THR* 5.8 0.8 - - - +
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Residues in contact with GLN 34 (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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30A ALA 2.9 19.4 + - - +
31A PHE* 3.4 15.5 + - - +
33A GLN* 1.3 77.6 - - - +
35A ASN* 1.3 74.4 + - - +
36A GLN* 4.7 3.1 - - - +
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Residues in contact with ASN 35 (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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12A ARG* 5.0 3.6 + - - -
14A TYR* 3.6 30.3 + - - +
31A PHE* 3.1 45.6 + - - +
34A GLN* 1.3 90.5 + - - +
36A GLN* 1.3 72.8 + - - +
37A LEU* 3.2 23.6 + - + +
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Residues in contact with GLN 36 (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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32A VAL 2.8 11.7 + - - -
33A GLN* 2.7 34.7 + - - +
34A GLN 4.7 3.1 - - - +
35A ASN* 1.3 80.4 - - - +
37A LEU* 1.3 64.1 + - - +
38A ARG* 3.5 13.4 + - - +
80A LEU* 3.7 33.7 - - + +
117A GLU* 4.3 2.3 - - - +
141A ARG* 5.1 1.9 + - - -
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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