Contacts of the helix formed by residues 18 - 33 (chain B) in PDB entry 5I1U
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 HIS 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ASN* 2.8 20.5 + - - +
17B PRO* 1.3 94.4 + - + +
19B GLN* 1.3 64.8 + - - +
20B THR 3.3 3.2 + - - -
21B GLU* 3.3 13.3 + - + +
22B ALA* 2.9 21.3 + - - +
61B SER 3.5 16.6 - - - -
62B SER* 3.9 3.8 - - - -
63B ALA* 3.6 38.4 + - + +
66B LEU* 3.7 5.8 - - + -
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Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 3.0 29.2 + - - -
16B ASN 3.3 10.5 + - - +
17B PRO 3.3 2.4 + - - -
18B HIS* 1.3 76.3 - - - +
20B THR* 1.3 59.3 + - - +
22B ALA* 3.4 1.7 + - - +
23B ALA* 2.9 30.1 + - + +
49B ASP* 4.5 3.4 + - - -
51B THR* 4.6 8.8 + - - +
52B GLU* 3.0 37.1 + - - +
55B SER* 3.3 31.0 - - - +
66B LEU* 3.7 5.2 - - - +
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Residues in contact with THR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO 5.1 1.0 + - - -
18B HIS 3.4 1.0 - - - -
19B GLN* 1.3 78.8 - - - +
21B GLU* 1.3 65.5 + - - +
23B ALA* 3.2 8.1 + - - +
24B ASP* 3.0 32.6 + - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS* 3.3 15.4 + - - +
20B THR* 1.3 79.8 - - - +
22B ALA* 1.3 63.3 + - - +
24B ASP* 3.2 9.3 + - - +
25B ARG* 3.1 56.7 + - + +
63B ALA* 3.4 23.5 - - + +
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Residues in contact with ALA 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 HIS 2.9 17.6 + - - +
19B GLN 3.8 2.2 - - - +
21B GLU* 1.3 76.6 - - - +
23B ALA* 1.3 57.7 + - - +
25B ARG* 3.2 4.3 + - - +
26B HIS* 2.8 30.3 + - - +
51B THR* 4.7 3.1 - - + -
63B ALA 4.0 6.2 + - - +
66B LEU* 3.6 33.2 - - + +
67B ALA* 3.8 24.7 - - - +
70B ALA* 5.5 2.5 - - + -
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Residues in contact with ALA 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 GLN* 2.9 19.7 + - + +
20B THR* 3.2 8.0 + - - +
22B ALA* 1.3 77.0 - - - +
24B ASP* 1.3 59.9 + - - +
26B HIS* 3.2 3.1 + - - +
27B LEU* 3.0 35.5 + - + +
51B THR* 3.6 31.9 - - + +
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Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 3.0 24.4 + - - +
21B GLU* 3.2 10.4 + - + +
23B ALA* 1.3 80.2 - - - +
25B ARG* 1.3 63.0 + - + +
27B LEU* 3.3 17.8 + - - +
28B GLU* 3.2 31.2 + - - +
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU* 3.1 50.2 + - + +
22B ALA* 3.6 5.6 - - - +
24B ASP* 1.3 76.8 - - + +
26B HIS* 1.3 61.7 + - - +
28B GLU* 3.2 18.0 + - - +
29B TRP* 3.1 20.3 + - - +
32B ARG* 5.3 0.3 + - - -
63B ALA* 4.3 7.2 + - - +
64B GLU* 3.9 36.6 - - - +
67B ALA* 3.7 24.7 - - + +
71B ASP* 4.4 2.0 - - - +
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Residues in contact with HIS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 2.8 17.2 + - - +
23B ALA 3.5 5.4 - - - +
24B ASP 3.2 0.2 - - - -
25B ARG* 1.3 76.0 - - - +
27B LEU* 1.3 62.1 + - + +
29B TRP* 3.2 9.3 + + - +
30B LEU* 3.0 43.6 + - + +
45B TYR* 2.5 33.9 + + - -
50B ILE* 4.0 5.2 - - + +
51B THR* 3.8 23.6 - - + -
67B ALA* 4.9 1.3 - - - +
70B ALA* 3.3 28.3 - - + -
71B ASP* 2.7 37.2 + - - +
74B GLY* 4.3 2.7 - - - -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA* 3.0 20.3 + - + +
24B ASP* 3.3 22.0 + - - +
26B HIS* 1.3 77.9 - - + +
28B GLU* 1.3 58.5 + - + +
30B LEU* 3.2 22.2 + - + +
31B GLN* 3.0 43.7 + - - +
46B THR* 6.4 2.0 - - + -
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Residues in contact with GLU 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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24B ASP* 3.2 18.9 + - - +
25B ARG* 3.4 17.4 - - - +
26B HIS 3.2 0.2 - - - -
27B LEU* 1.3 77.1 - - + +
29B TRP* 1.3 62.1 + - - +
31B GLN* 3.2 19.6 + - - +
32B ARG* 3.0 39.5 + - - +
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Residues in contact with TRP 29 (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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25B ARG 3.1 9.8 + - - +
26B HIS* 3.2 9.4 + + - +
28B GLU* 1.3 76.8 - - - +
30B LEU* 1.3 86.2 + - + +
32B ARG* 3.1 22.4 + - - +
33B HIS* 3.0 50.6 + + + -
36B LEU* 4.4 5.6 - - + -
71B ASP* 3.2 51.4 - - + +
75B PHE* 4.2 15.9 - - + -
78B LEU* 4.6 5.4 - - + -
119B ALA* 3.9 29.2 - - + -
122B ASP* 2.9 22.6 + - - -
123B LEU* 4.1 17.4 - - + +
126B ARG* 3.4 22.0 - - - +
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Residues in contact with LEU 30 (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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26B HIS* 3.0 40.0 + - + +
27B LEU* 3.2 24.6 + - + +
29B TRP* 1.3 90.3 - - + +
31B GLN* 1.3 62.8 + - + +
33B HIS 3.2 4.9 - - - +
34B ARG* 3.1 22.7 + - - -
37B ALA* 3.8 27.1 - - + +
45B TYR* 3.6 36.8 - - + +
78B LEU* 4.0 13.5 - - + -
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Residues in contact with GLN 31 (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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27B LEU* 3.0 32.2 + - - +
28B GLU* 3.4 19.3 - - - +
30B LEU* 1.3 78.4 - - + +
32B ARG* 1.3 59.8 + - - +
33B HIS 3.4 0.7 + - - -
34B ARG* 3.5 18.3 + - - +
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Residues in contact with ARG 32 (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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25B ARG 5.3 0.4 + - - -
28B GLU* 3.0 37.6 + - - +
29B TRP* 3.1 32.7 + - - +
31B GLN* 1.3 75.8 - - - +
33B HIS* 1.3 71.0 + - + +
34B ARG* 3.4 2.5 + - - +
118B ARG* 4.0 30.0 + - - +
122B ASP* 5.0 6.2 + - - -
126B ARG* 5.6 0.6 - - - +
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Residues in contact with HIS 33 (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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29B TRP* 3.0 67.9 + + + +
30B LEU* 3.2 5.2 - - + -
32B ARG* 1.3 89.8 + - + +
34B ARG* 1.3 64.8 + - - +
35B GLU 3.3 2.5 - - - -
36B LEU* 3.3 14.9 + - + -
37B ALA* 3.0 21.0 + - - +
78B LEU* 5.9 0.2 - - - +
115B PRO 4.9 1.2 + - - +
118B ARG* 3.7 44.0 + - + +
119B ALA* 3.7 25.9 + - + +
122B ASP* 4.3 11.6 - - + +
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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