Contacts of the helix formed by residues 17 - 28 (chain B) in PDB entry 4TXQ
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 ILE 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 4.7 0.2 - - + -
14B PHE* 3.1 39.0 - - + +
16B SER* 1.3 83.7 - - - +
18B GLN* 1.3 64.3 + - - +
19B HIS 3.3 2.5 - - - -
20B HIS* 3.3 11.3 + - + +
21B LEU* 3.1 34.4 + - + +
41B TYR* 4.5 7.6 - - + +
42B ALA* 3.5 39.9 - - + +
45B THR* 3.6 36.6 - - + -
46B GLY* 4.6 3.6 - - - -
49B ILE* 4.7 2.7 - - + -
59B PHE* 5.0 4.0 - - + -
60B LEU* 5.8 0.2 - - + -
63B LEU* 5.4 0.4 - - + -
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Residues in contact with GLN 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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10B LEU* 3.6 28.0 - - + +
14B PHE 3.6 2.8 + - - -
15B LYS* 2.7 49.1 + - - +
16B SER 3.4 0.6 - - - -
17B ILE* 1.3 78.4 - - - +
19B HIS* 1.3 75.4 + - + +
21B LEU* 3.4 5.6 + - - +
22B ARG* 3.0 26.6 + - + +
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Residues in contact with HIS 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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15B LYS* 5.0 3.9 + - - -
16B SER 5.0 0.8 + - - -
17B ILE 3.3 0.6 - - - -
18B GLN* 1.3 100.2 + - + +
20B HIS* 1.3 59.4 + - + +
22B ARG* 3.3 9.4 + - + +
23B THR* 2.6 38.4 + - - -
119B TYR* 2.6 34.6 + + + +
123B LEU* 3.8 22.4 - - + -
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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
----------------------------------------------------------
16B SER 3.4 17.7 + - - -
17B ILE* 3.3 20.6 + - + +
19B HIS* 1.3 78.9 + - + +
21B LEU* 1.3 58.2 + - - +
23B THR* 3.2 9.6 + - - -
24B ALA 2.9 23.2 + - - -
38B CYS* 3.6 19.1 - - - +
41B TYR* 3.5 37.1 - + + -
42B ALA* 5.1 1.6 - - + -
123B LEU* 3.5 40.7 - - + +
126B ASP* 2.8 30.1 + - - +
127B VAL* 4.1 7.6 - - + -
146B ARG* 5.5 0.2 - - - -
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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
----------------------------------------------------------
7B LEU* 4.9 8.1 - - + -
10B LEU* 3.7 31.4 - - + -
17B ILE* 3.1 24.3 + - + +
18B GLN 3.6 6.5 - - - +
20B HIS* 1.3 73.9 - - - +
22B ARG* 1.3 64.3 + - - +
24B ALA* 3.2 5.8 + - - +
25B GLN* 3.0 30.4 + - - +
38B CYS* 5.6 0.2 - - - -
39B ARG* 4.6 11.9 - - + -
42B ALA* 3.6 23.3 - - + -
59B PHE* 3.7 17.9 - - + -
63B LEU* 4.1 21.5 - - + -
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Residues in contact with ARG 22 (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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18B GLN* 3.0 15.5 + - + +
19B HIS* 3.7 15.7 - - + +
21B LEU* 1.3 75.9 - - - +
23B THR* 1.3 57.6 + - - +
25B GLN* 3.1 24.1 + - - +
26B GLU* 2.9 66.4 + - - +
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Residues in contact with THR 23 (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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19B HIS 2.6 24.9 + - - -
20B HIS* 3.2 8.2 + - - -
22B ARG* 1.3 76.2 - - - +
24B ALA* 1.3 63.7 + - - +
26B GLU* 3.4 9.3 + - - +
27B HIS* 2.8 50.6 + - + +
38B CYS* 3.9 18.2 - - - -
120B THR* 4.3 16.7 + - + +
123B LEU* 3.5 21.5 - - + +
124B LEU* 4.7 7.4 - - + -
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Residues in contact with ALA 24 (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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20B HIS 2.9 7.9 + - - +
21B LEU* 3.4 11.2 - - + +
22B ARG 3.2 0.2 - - - -
23B THR* 1.3 76.1 - - - +
25B GLN* 1.3 62.9 + - + +
27B HIS 3.1 2.1 + - - -
28B ASP* 3.0 23.0 + - - -
35B ALA* 3.5 35.8 - - - +
38B CYS* 3.6 18.7 - - + +
39B ARG* 3.9 21.3 - - + +
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Residues in contact with GLN 25 (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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7B LEU* 6.5 0.9 - - - -
21B LEU* 3.0 23.4 + - - +
22B ARG* 3.1 28.7 + - - +
24B ALA* 1.3 75.5 - - - +
26B GLU* 1.3 62.5 + - - +
27B HIS 3.2 0.7 + - - -
28B ASP* 3.3 27.3 + - - +
29B LYS 4.9 0.5 + - - -
39B ARG* 4.7 7.9 - - - +
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Residues in contact with GLU 26 (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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22B ARG* 2.9 65.9 + - - +
23B THR* 3.8 10.2 - - - +
24B ALA 3.3 0.2 - - - -
25B GLN* 1.3 77.1 - - - +
27B HIS* 1.3 70.9 + - + +
28B ASP 3.5 0.4 + - - -
29B LYS* 4.8 4.0 + - - +
30B ARG* 5.2 3.6 + - - +
116B LYS* 3.5 33.7 + - - -
120B THR* 5.7 0.2 + - - -
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Residues in contact with HIS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B THR* 2.8 43.0 + - + +
24B ALA 3.1 5.3 + - - +
26B GLU* 1.3 90.8 - - + +
28B ASP* 1.3 60.6 + - - +
29B LYS 3.1 3.6 - - - -
30B ARG* 4.1 5.6 - - + +
31B ASP* 2.8 59.0 + - + +
34B VAL* 3.8 8.9 - - + +
35B ALA* 4.0 8.3 - - - +
93B TYR* 2.6 44.3 + + - -
120B THR* 4.9 7.4 - - + -
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Residues in contact with ASP 28 (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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1B MET* 4.6 5.8 - - - +
24B ALA 3.0 9.5 + - - -
25B GLN* 3.3 19.9 + - - +
27B HIS* 1.3 78.0 - - - +
29B LYS* 1.3 61.8 + - - +
32B PRO* 3.8 17.2 - - - +
35B ALA* 3.1 11.0 - - - +
39B ARG* 2.6 48.0 + - - -
70B LEU* 4.4 3.6 - - - +
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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