Contacts of the helix formed by residues 23 - 34 (chain M) in PDB entry 4UJ3
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 GLY 23 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21M GLY 3.2 3.8 - - - -
22M VAL* 1.3 79.2 - - - +
24M LYS* 1.3 66.5 + - - +
26M ASN* 3.2 4.7 + - - +
27M LEU* 3.0 26.8 + - - +
124M ASN* 3.7 6.0 + - - -
200M GNP 3.2 38.5 + - - -
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Residues in contact with LYS 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M LEU* 3.4 29.9 - - + +
17M ILE* 3.6 26.9 - - - +
18M GLY* 3.1 11.7 + - - +
19M ASP 2.8 27.1 + - - -
22M VAL* 3.4 13.6 - - + +
23M GLY* 1.3 72.4 - - - +
25M SER* 1.3 62.0 + - - +
27M LEU* 3.0 14.2 + - - +
28M LEU 3.0 17.7 + - - -
66M ASP* 4.0 7.9 - - - +
67M THR* 3.4 17.7 - - - -
69M GLY* 3.6 4.6 - - - +
90M VAL* 4.1 11.9 - - + -
200M GNP 2.7 46.7 + - - +
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Residues in contact with SER 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M LYS* 1.3 76.1 - - - +
26M ASN* 1.3 59.3 + - - +
28M LEU* 3.4 5.5 - - - +
29M SER* 3.1 25.1 + - - -
40M SER* 5.2 3.4 - - - -
41M LYS 5.5 2.0 - - - -
43M THR* 2.5 13.1 + - - -
66M ASP* 2.9 16.5 + - - -
200M GNP 2.4 19.0 + - - -
201M MG 1.9 33.1 - - - -
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Residues in contact with ASN 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M GLY 3.7 5.8 - - - +
24M LYS 3.1 0.4 - - - -
25M SER* 1.3 74.4 - - - +
27M LEU* 1.3 60.7 + - - +
28M LEU 3.1 1.1 - - - -
29M SER* 3.2 6.1 + - - -
30M ARG* 2.8 33.3 + - - +
35M GLU 4.1 0.3 - - - +
36M PHE* 3.1 25.4 - - + -
37M ASN* 2.7 38.4 + - - +
40M SER* 3.0 23.9 + - - -
155M ALA* 3.8 8.5 - - + -
200M GNP 2.8 39.5 + - + +
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Residues in contact with LEU 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M LEU* 4.8 7.0 - - + -
23M GLY 3.0 17.8 + - - +
24M LYS* 3.3 9.2 - - - +
26M ASN* 1.3 76.7 - - - +
28M LEU* 1.3 63.9 + - - +
30M ARG* 3.9 2.0 - - - +
31M PHE* 3.1 26.3 + - - +
88M LEU* 5.6 3.8 - - + -
90M VAL* 3.9 35.4 - - + -
122M VAL* 4.6 7.2 - - + -
124M ASN* 3.9 16.4 - - + +
153M THR* 3.6 25.1 - - + +
155M ALA* 4.0 4.0 - - + +
161M VAL* 4.0 27.2 - - + +
164M ALA* 6.2 1.1 - - + -
165M PHE* 3.8 16.5 - - + -
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Residues in contact with LEU 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M LEU* 4.0 9.8 - - + +
24M LYS 3.0 11.0 + - - +
25M SER* 3.4 10.1 - - - +
27M LEU* 1.3 77.7 - - - +
29M SER* 1.3 59.0 + - - +
31M PHE* 4.0 0.4 - - - -
32M THR* 2.7 38.1 + - + +
47M GLU* 4.7 11.9 - - + +
48M PHE* 5.0 3.1 - - - -
49M ALA* 3.7 26.2 - - + +
64M ILE* 3.5 43.3 - - + +
66M ASP* 3.6 29.4 - - + +
165M PHE* 5.0 4.0 - - - -
755O VAL* 5.4 3.1 - - + -
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Residues in contact with SER 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M SER 3.1 8.0 + - - -
26M ASN* 3.2 21.3 + - - -
28M LEU* 1.3 80.8 - - - +
30M ARG* 1.3 58.0 + - - +
32M THR* 3.9 5.2 - - - -
33M ARG* 2.9 28.1 + - - -
34M ASN 3.0 6.4 + - - -
35M GLU* 2.5 37.9 + - - -
36M PHE* 4.2 0.3 - - - -
37M ASN* 4.9 0.9 + - - +
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Residues in contact with ARG 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M ASN 2.8 20.1 + - - +
27M LEU* 3.9 4.3 - - - +
29M SER* 1.3 77.5 - - - +
31M PHE* 1.3 58.9 + - - +
34M ASN* 2.9 56.8 + - - +
35M GLU* 3.1 8.5 + - - +
36M PHE* 3.2 24.3 - - - +
51M ARG* 5.3 0.5 + - - -
155M ALA* 2.9 20.2 + - - +
156M LEU 2.9 26.5 + - - -
158M SER* 2.9 26.1 + - - -
161M VAL* 3.5 33.0 - - + -
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Residues in contact with PHE 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M LEU 3.1 6.9 + - - +
28M LEU 4.0 1.3 - - - +
30M ARG* 1.3 83.1 - - - +
32M THR* 1.3 71.7 + - + +
34M ASN* 4.5 0.9 + - - +
51M ARG* 3.0 72.1 + - + +
53M ILE* 4.3 14.1 - - + -
62M ALA* 4.6 8.5 - - + -
64M ILE* 4.4 11.0 - - + -
161M VAL* 4.1 9.8 - - + +
162M GLU* 3.8 16.4 - - - -
165M PHE* 3.3 69.8 - + + -
166M GLN* 5.1 2.2 - - + -
169M LEU* 4.6 6.1 - - + -
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Residues in contact with THR 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M LEU* 2.7 32.6 + - + +
29M SER* 3.9 3.3 - - - -
31M PHE* 1.3 92.0 - - + +
33M ARG* 1.3 64.2 + - - +
34M ASN 3.7 0.2 - - - -
49M ALA* 3.6 40.8 - - + +
50M THR 4.1 15.9 - - - +
51M ARG* 4.5 8.8 - - + +
64M ILE* 4.7 2.5 - - + -
756O LYS* 5.5 2.9 - - - -
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Residues in contact with ARG 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M SER* 2.9 13.1 + - - +
32M THR* 1.3 81.5 + - - +
34M ASN* 1.3 71.8 + - - +
35M GLU* 3.0 30.4 + - + +
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Residues in contact with ASN 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M ARG* 2.9 55.0 + - - +
31M PHE 4.4 1.2 + - - +
32M THR 3.7 1.2 - - - -
33M ARG* 1.3 78.0 - - - +
35M GLU* 1.3 60.1 + - - +
158M SER* 4.3 2.1 + - - -
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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