Contacts of the helix formed by residues 25 - 39 (chain A) in PDB entry 2JXP
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 LEU 25 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 4.2 8.1 - - + +
22A PRO* 4.2 17.0 - - + -
23A ALA* 3.9 20.2 - - + +
24A GLY* 1.3 87.6 - - - +
26A THR* 1.3 67.9 + - - +
27A ILE* 3.2 14.6 - - + +
28A GLY* 2.9 15.9 + - - -
29A SER* 4.1 2.4 + - - -
56A ILE* 4.5 8.3 - - + -
58A HIS* 5.0 2.0 - - - -
59A ALA* 3.8 42.8 - - + +
60A ILE* 6.0 0.9 - - + -
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Residues in contact with THR 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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25A LEU* 1.3 71.7 - - - +
27A ILE* 1.3 60.7 + - - +
29A SER* 2.8 33.1 + - - -
30A ASP* 3.0 18.4 + - - +
129A GLN* 4.8 10.6 + - - -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 16.6 - - + -
26A THR* 1.3 82.1 + - - +
28A GLY* 1.3 59.9 + - - +
29A SER 3.3 0.2 - - - -
30A ASP* 3.9 9.6 + - + -
31A LEU* 2.9 32.6 + - + +
56A ILE* 3.6 36.1 - - + -
59A ALA* 4.6 4.3 - - + -
81A TYR* 4.2 20.2 - - - +
83A VAL* 4.6 7.6 - - + -
129A GLN* 4.8 7.9 - - - +
132A ALA* 5.3 3.4 - - + -
133A VAL* 4.8 18.6 - - + +
136A ILE* 3.7 30.1 - - + -
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Residues in contact with GLY 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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19A ILE* 3.6 23.6 - - - +
21A ALA* 5.5 7.4 - - - -
25A LEU 2.9 13.0 + - - -
26A THR 2.8 0.6 + - - -
27A ILE* 1.3 83.2 - - - +
29A SER* 1.3 59.5 + - - +
31A LEU* 5.5 0.2 - - - -
32A GLU* 3.3 30.5 + - - +
56A ILE* 6.4 0.7 - - - -
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU 4.1 2.4 + - - -
26A THR* 2.8 18.1 + - - -
28A GLY* 1.3 69.2 - - - -
30A ASP* 1.3 67.5 + - - +
32A GLU* 3.6 12.6 + - - +
33A ARG* 3.4 47.2 + - - +
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Residues in contact with ASP 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 THR* 3.0 22.9 + - - +
27A ILE* 3.7 10.3 - - - +
29A SER* 1.3 77.2 - - - +
31A LEU* 1.3 57.8 + - - +
33A ARG* 3.2 13.5 + - - +
34A VAL* 2.9 35.6 + - + +
129A GLN* 5.4 12.1 - - - +
130A LYS* 5.8 2.1 + - - -
133A VAL* 4.1 19.6 - - + +
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Residues in contact with LEU 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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19A ILE* 3.7 24.2 - - + -
27A ILE* 2.9 24.2 + - + +
28A GLY* 3.8 5.6 - - - +
29A SER 3.3 0.2 - - - -
30A ASP* 1.3 73.5 - - - +
32A GLU* 1.3 63.9 + - - +
34A VAL* 3.2 2.7 + - + +
35A ILE* 2.9 53.0 + - + +
54A ILE* 3.9 28.5 - - + -
133A VAL* 3.6 24.8 - - + +
136A ILE* 4.3 26.5 - - + -
137A LEU* 5.1 4.3 - - + +
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Residues in contact with GLU 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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19A ILE* 4.0 16.8 - - + +
28A GLY 3.3 18.4 + - - +
29A SER* 4.0 11.6 + - - +
30A ASP 3.4 0.8 - - - -
31A LEU* 1.3 76.1 - - - +
33A ARG* 1.3 59.8 + - + +
35A ILE* 3.5 2.0 + - - +
36A SER* 3.0 30.3 + - - -
43A VAL* 3.4 45.6 - - + +
44A VAL 5.3 0.7 - - - +
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Residues in contact with ARG 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 SER* 3.4 33.3 + - - +
30A ASP* 3.2 13.1 + - - +
32A GLU* 1.3 75.5 - - + +
34A VAL* 1.3 65.7 + - + +
36A SER* 3.4 4.2 + - - -
37A THR* 2.9 37.0 + - + +
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Residues in contact with VAL 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 ASP* 2.9 27.5 + - + +
31A LEU* 3.7 3.8 - - + +
33A ARG* 1.3 73.1 - - + +
35A ILE* 1.3 58.2 + - + +
37A THR* 3.1 5.8 + - - -
38A HIS* 3.0 33.3 + - + +
133A VAL* 3.8 26.9 - - + +
134A GLN* 3.3 32.5 - - - +
137A LEU* 3.6 28.9 - - + -
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Residues in contact with ILE 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 LEU* 6.2 0.9 - - + -
17A VAL* 4.2 11.7 - - + -
19A ILE* 6.3 2.0 - - + -
31A LEU* 2.9 46.6 + - + +
32A GLU 3.7 3.6 - - - +
34A VAL* 1.3 75.9 - - - +
36A SER* 1.3 59.1 + - - +
39A THR* 2.8 52.6 + - + +
41A ALA* 3.6 21.3 - - + +
43A VAL* 4.2 17.9 - - + -
54A ILE* 3.8 24.2 - - + -
137A LEU* 4.0 17.7 - - + -
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Residues in contact with SER 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 GLU 3.0 18.4 + - - -
33A ARG* 4.0 5.2 - - - -
35A ILE* 1.3 77.1 - - - +
37A THR* 1.3 63.3 + - - +
39A THR 3.5 10.4 - - - +
41A ALA 3.9 13.9 - - - +
42A LYS* 3.8 26.6 + - - +
43A VAL* 5.8 2.7 - - - -
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Residues in contact with THR 37 (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 VAL* 4.7 6.1 - - - +
33A ARG* 2.9 25.7 + - + +
34A VAL* 3.1 7.3 + - - -
36A SER* 1.3 82.3 - - - +
38A HIS* 1.3 75.7 + - - +
39A THR 4.6 0.9 - - - +
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Residues in contact with HIS 38 (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 VAL* 3.3 16.6 - - + +
10A SER* 3.2 47.6 + - - -
11A GLU* 3.4 2.1 - - - +
34A VAL* 3.0 27.0 + - + +
37A THR* 1.3 103.4 + - - +
39A THR* 1.3 60.8 + - + +
134A GLN* 3.7 26.0 + - - -
137A LEU* 3.6 18.9 - - + +
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Residues in contact with THR 39 (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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10A SER 3.2 20.2 - - - +
11A GLU* 3.6 14.6 - - - +
12A LEU* 4.0 20.6 - - + -
35A ILE* 2.8 29.0 + - + +
36A SER 3.5 12.5 - - - +
37A THR 4.6 0.7 - - - +
38A HIS* 1.3 74.5 - - - +
40A ARG* 1.3 61.7 + - - +
41A ALA* 3.0 24.6 + - - +
42A LYS* 5.0 0.9 + - - -
137A LEU* 3.4 31.0 - - + -
141A SER* 5.6 0.4 - - - -
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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