Contacts of the helix formed by residues 24 - 35 (chain A) in PDB entry 2JG3
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 PRO 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A THR* 1.4 91.8 - - + +
25A PRO* 1.4 65.9 - - + +
26A GLU* 3.2 18.8 - - + +
27A VAL* 3.0 34.4 + - + +
28A VAL* 3.1 9.7 + - - +
195A VAL 3.5 24.5 - - - +
196A PHE* 3.7 17.3 - - + -
197A PRO* 4.3 14.6 - - + -
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Residues in contact with PRO 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 THR 3.5 5.1 - - - +
24A PRO* 1.4 82.7 - - + +
26A GLU* 1.3 74.4 + - - +
28A VAL* 3.2 9.4 + - + +
29A ASP* 2.9 39.7 + - - +
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Residues in contact with GLU 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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24A PRO* 3.2 26.6 - - + +
25A PRO* 1.3 88.6 - - - +
27A VAL* 1.3 59.4 + - + +
29A ASP* 3.9 6.9 - - - +
30A PHE* 3.1 27.7 + - - +
222A GLU* 4.0 14.1 - - - +
223A SER 6.0 0.2 - - - +
224A GLU 6.1 0.2 - - - +
226A GLY* 4.6 15.3 - - - -
227A PHE* 3.7 28.1 + - + -
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Residues in contact with VAL 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 THR* 3.6 19.7 - - + -
24A PRO* 3.0 26.5 + - + +
26A GLU* 1.3 77.1 - - + +
28A VAL* 1.3 63.7 + - - +
30A PHE* 3.5 4.5 + - - +
31A MET* 3.0 38.7 + - + +
163A VAL* 4.4 9.0 - - + -
192A LEU* 4.1 19.1 - - + -
195A VAL* 3.9 28.3 - - + -
196A PHE* 5.5 0.2 - - + -
227A PHE* 4.0 18.6 - - + -
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Residues in contact with VAL 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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23A THR* 3.8 28.0 - - - +
24A PRO 3.1 13.8 + - - +
25A PRO* 3.5 9.6 - - + +
27A VAL* 1.3 76.4 - - - +
29A ASP* 1.3 58.9 + - - +
31A MET* 3.2 2.4 + - - +
32A VAL* 2.8 38.9 + - + +
52A PRO* 4.2 14.6 - - + +
53A PHE* 3.8 29.4 - - + -
56A ALA* 3.6 29.8 - - + -
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Residues in contact with ASP 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 PRO* 2.9 27.5 + - - +
26A GLU* 3.9 7.1 - - - +
28A VAL* 1.3 78.0 - - - +
30A PHE* 1.3 64.3 + - - +
32A VAL* 3.3 6.1 + - - +
33A SER* 3.0 23.4 + - - -
56A ALA* 4.7 8.1 - - - +
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Residues in contact with PHE 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 GLU 3.1 19.3 + - - +
27A VAL* 3.7 4.3 - - - +
29A ASP* 1.3 76.1 - - - +
31A MET* 1.3 64.0 + - - +
33A SER* 2.6 32.0 + - - -
34A LEU* 3.3 25.8 + - + +
190A TYR* 3.8 38.4 - + + -
192A LEU* 4.2 15.5 - - + -
205A VAL* 4.0 19.5 - - + -
220A THR* 4.1 8.3 - - + -
227A PHE* 3.7 33.4 - + + +
229A PRO* 3.5 31.2 - - + -
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Residues in contact with MET 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 VAL* 3.0 26.6 + - - +
28A VAL 3.7 3.6 - - - +
30A PHE* 1.3 74.6 - - - +
32A VAL* 1.3 58.1 + - - +
34A LEU* 3.0 22.7 + - - +
35A ALA* 3.2 12.9 + - - +
53A PHE* 3.4 28.5 - - + -
103A LEU* 5.5 2.5 - - + -
104A GLY 3.2 27.1 - - - +
161A VAL* 3.3 37.9 - - + +
162A PHE 3.6 1.8 - - - -
163A VAL* 3.4 32.8 - - - +
205A VAL* 3.9 20.6 - - + -
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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 VAL* 2.8 28.7 + - + +
29A ASP* 3.8 6.5 - - - +
31A MET* 1.3 72.1 - - - +
33A SER* 1.3 61.1 + - - +
35A ALA* 3.1 25.5 + - - +
53A PHE* 4.5 3.8 - - + +
56A ALA* 3.9 31.2 - - + +
57A PHE* 4.0 17.9 - - + +
60A ALA* 3.8 27.8 - - + -
61A HIS* 3.8 8.0 - - + -
103A LEU* 4.3 17.3 - - + -
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Residues in contact with SER 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 ASP 3.0 14.0 + - - -
30A PHE* 2.6 31.9 + - - -
32A VAL* 1.3 74.9 - - - +
34A LEU* 1.3 64.7 + - - +
35A ALA 3.4 2.3 - - - +
61A HIS* 5.8 1.1 - - - -
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Residues in contact with LEU 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 PHE* 3.5 33.7 - - + +
31A MET* 3.0 8.9 + - - +
33A SER* 1.3 84.5 - - - +
35A ALA* 1.3 61.9 + - - +
36A GLU* 4.5 3.6 - - - +
159A VAL* 4.8 0.2 - - - +
161A VAL* 4.3 11.3 - - + +
190A TYR* 3.6 46.9 - - + +
205A VAL* 3.8 23.3 - - + -
207A ARG* 3.1 36.2 + - + +
229A PRO* 5.1 4.9 - - + -
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Residues in contact with ALA 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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31A MET 3.2 9.6 + - - +
32A VAL* 3.1 15.5 + - - +
33A SER 4.7 2.3 - - - +
34A LEU* 1.3 78.9 - - - +
36A GLU* 1.3 67.1 + - - +
57A PHE* 3.9 21.1 - - + -
61A HIS* 3.5 19.1 - - - -
101A LEU* 3.9 17.7 - - + -
103A LEU* 4.4 6.3 - - + -
159A VAL* 5.0 0.4 - - - -
161A VAL* 4.1 10.1 - - + -
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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