Contacts of the helix formed by residues 9 - 21 (chain B) in PDB entry 4XJO
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 THR 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 1.3 74.4 - - - +
10B PRO* 1.4 68.2 - - - +
11B GLU* 3.6 8.7 + - - +
12B GLN* 3.0 38.1 + - - +
13B ILE* 2.8 28.3 + - - +
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Residues in contact with PRO 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU 4.6 0.9 - - - +
9B THR* 1.4 85.6 - - - +
11B GLU* 1.3 58.3 + - + +
13B ILE* 3.3 13.6 + - + +
14B ILE* 3.0 33.5 + - - +
37B VAL* 3.8 11.6 - - + +
39B VAL* 5.0 5.6 - - + -
49B ILE* 3.9 45.3 - - + -
52B GLY* 5.6 3.8 - - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B THR* 3.2 8.1 + - - +
10B PRO* 1.3 80.8 - - + +
12B GLN* 1.3 62.5 + - + +
14B ILE* 3.3 9.2 + - - +
15B ALA* 3.1 22.2 + - - +
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Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.4 26.4 - - + +
9B THR* 3.0 43.3 + - - +
11B GLU* 1.3 73.6 - - + +
13B ILE* 1.3 66.3 + - - +
15B ALA* 3.3 7.0 + - - +
16B VAL* 3.0 30.6 + - + +
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR* 3.8 26.0 - - + +
97A HIS 4.0 15.5 - - - +
98A GLU* 3.7 33.9 - - + +
101A ALA* 4.0 13.9 - - + +
8B LEU* 3.8 24.0 - - + +
9B THR 2.8 21.4 + - - +
10B PRO* 3.5 7.9 - - + +
12B GLN* 1.3 76.1 - - - +
14B ILE* 1.3 58.2 + - - +
16B VAL* 3.4 1.2 + - - +
17B ASP* 2.8 31.7 + - - +
37B VAL* 4.0 21.3 - - + -
39B VAL* 5.7 2.9 - - + -
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Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR* 4.3 8.5 - - + -
10B PRO 3.0 17.8 + - - +
11B GLU* 3.6 9.9 - - - +
12B GLN 3.3 0.2 - - - -
13B ILE* 1.3 76.3 - - - +
15B ALA* 1.3 56.8 + - - +
17B ASP* 3.7 2.9 - - + +
18B GLY* 2.9 27.4 + - - -
34B SER* 4.4 22.0 - - - +
35B PRO* 3.3 30.7 - - + +
37B VAL* 3.7 20.2 - - + +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU 3.1 13.2 + - - +
12B GLN* 3.7 9.6 - - - +
13B ILE 3.3 0.2 - - - -
14B ILE* 1.3 75.7 - - - +
16B VAL* 1.3 65.8 + - + +
18B GLY* 3.5 0.7 + - - -
19B ALA* 3.3 23.2 + - - +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA* 3.4 34.5 - - + +
104A ALA* 4.7 5.2 - - + -
105A LYS* 4.2 26.7 - - + +
8B LEU* 4.4 18.6 - - + -
12B GLN* 3.0 20.7 + - + +
13B ILE 3.9 3.4 - - - +
15B ALA* 1.3 75.8 - - + +
17B ASP* 1.3 58.4 + - - +
19B ALA 3.2 1.7 + - - -
20B HIS* 2.9 48.3 + - + +
21B LEU* 5.2 0.2 - - + -
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Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR* 2.7 23.4 + - + +
13B ILE* 2.8 20.0 + - + +
14B ILE* 3.7 6.0 - - - +
16B VAL* 1.3 77.1 - - - +
18B GLY* 1.3 66.1 + - - +
21B LEU* 3.0 46.0 + - + +
23B HIS* 2.6 31.8 + - - -
35B PRO* 3.3 27.7 - - - +
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Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE 2.9 17.3 + - - -
15B ALA* 4.0 1.3 - - - -
17B ASP* 1.3 80.9 + - - +
19B ALA* 1.3 59.1 + - - +
21B LEU 5.2 0.2 + - - -
28B ILE* 4.3 14.6 - - - +
29B GLY* 4.4 10.4 + - - -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASP* 3.6 5.7 - - - +
117A THR* 3.9 11.6 - - - +
15B ALA 3.3 15.6 + - - +
16B VAL* 3.2 1.8 + - - -
18B GLY* 1.3 78.3 - - - +
20B HIS* 1.3 87.3 + - + +
28B ILE* 4.2 7.9 - - - +
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Residues in contact with HIS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA* 4.4 13.0 - - + -
105A LYS* 5.1 12.7 - - + +
108A VAL* 3.9 30.8 - - + +
116A ASP* 2.7 32.1 + - + +
117A THR* 4.1 4.5 - - - +
118A VAL* 2.7 35.2 + - - +
16B VAL* 2.9 37.0 + - + +
19B ALA* 1.3 97.5 + - + +
21B LEU* 1.3 58.2 + - - +
28B ILE* 4.5 0.7 - - - -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.2 12.1 - - + -
96A THR* 4.0 6.5 - - - +
100A ALA* 3.9 24.0 - - + +
101A ALA* 3.9 9.0 - - - +
104A ALA* 3.7 24.9 - - + -
118A VAL 3.9 7.9 - - - +
120A PHE* 3.7 27.1 - - + -
16B VAL 5.1 0.4 - - - +
17B ASP* 3.0 52.6 + - + +
19B ALA 4.0 0.2 - - - -
20B HIS* 1.3 75.6 - - + +
22B TRP* 1.3 63.7 + - - +
23B HIS* 3.6 12.3 + - - +
27B SER 4.7 2.6 - - - +
28B ILE* 3.4 12.8 - - - +
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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