Contacts of the helix formed by residues 27 - 39 (chain B) in PDB entry 4HRO
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 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ASP 4.5 5.4 - - - +
26B ALA* 1.3 77.6 - - - +
28B VAL* 1.3 63.9 + - - +
29B GLY* 3.7 0.9 - - - -
30B ASP* 3.0 32.4 + - - +
31B ALA* 2.9 22.2 + - - +
68B LEU 3.2 16.3 + - - +
69B GLY* 3.9 18.4 - - - +
70B GLU 3.1 9.9 - - - +
71B ALA* 4.5 1.8 - - - +
72B THR* 3.7 3.3 - - - +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TRP* 4.1 7.3 - - + -
27B THR* 1.3 72.4 - - - +
29B GLY* 1.3 58.4 + - - +
31B ALA* 3.1 4.8 + - - +
32B LEU* 2.8 26.5 + - - +
59B VAL* 3.8 29.6 - - + -
61B ARG* 4.2 16.4 - - - -
66B ALA* 4.5 3.8 - - + -
67B ALA 3.3 24.0 - - - +
68B LEU* 4.4 8.5 - - + -
70B GLU* 2.8 29.6 + - + +
72B THR* 3.6 18.6 - - + +
78B LEU* 4.5 8.1 - - + -
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Residues in contact with GLY 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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27B THR* 3.7 1.3 - - - -
28B VAL* 1.3 77.1 - - - +
30B ASP* 1.3 56.5 + - - +
32B LEU* 3.3 5.6 + - - +
33B ASP* 2.9 33.6 + - - +
68B LEU* 2.9 41.0 + - - +
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Residues in contact with ASP 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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22B VAL* 4.8 1.9 - - + +
25B ASP 4.4 1.2 - - - +
26B ALA* 3.5 17.4 - - + -
27B THR* 3.0 43.4 + - - +
29B GLY* 1.3 76.3 - - - +
31B ALA* 1.3 56.9 + - - +
33B ASP* 3.2 12.7 + - - +
34B ALA* 2.9 27.0 + - - +
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Residues in contact with ALA 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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1B MET* 4.1 15.9 - - - -
3B TRP* 3.0 18.3 + - - +
20B VAL* 4.5 2.0 - - + +
22B VAL* 4.2 16.2 - - + -
26B ALA* 4.8 0.6 - - - +
27B THR 2.9 12.5 + - - +
28B VAL* 3.1 9.4 + - - +
30B ASP* 1.3 75.3 - - - +
32B LEU* 1.3 57.2 + - - +
34B ALA* 3.3 3.1 + - - +
35B LEU 3.0 18.0 + - - -
72B THR* 4.3 1.1 - - + -
78B LEU* 3.6 27.8 - - + -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TRP* 3.5 17.4 - - + -
28B VAL 2.8 12.8 + - - +
29B GLY* 3.5 9.4 - - - +
30B ASP 3.2 0.2 - - - -
31B ALA* 1.3 74.3 - - - +
33B ASP* 1.3 64.8 + - - +
35B LEU* 3.2 14.6 + - + +
36B VAL* 3.0 25.7 + - + +
46B VAL* 3.9 12.8 - - + -
47B PHE* 3.9 16.6 - - + -
53B LEU* 3.9 28.3 - - + -
59B VAL* 5.1 2.5 - - + -
68B LEU* 4.2 18.6 - - + -
80B LEU* 3.9 33.2 - - + -
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Residues in contact with ASP 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 GLY 2.9 17.3 + - - +
30B ASP* 3.2 14.9 + - - +
32B LEU* 1.3 76.0 - - - +
34B ALA* 1.3 57.4 + - - +
36B VAL* 3.4 5.4 + - - +
37B GLY* 2.9 25.5 + - - -
47B PHE* 3.5 26.0 - - - -
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Residues in contact with ALA 34 (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 VAL* 4.2 12.7 - - + +
21B ASP 5.0 2.7 - - - +
22B VAL* 3.7 24.7 - - + -
30B ASP 2.9 13.2 + - - +
31B ALA 3.5 8.5 - - - +
32B LEU 3.2 0.2 - - - -
33B ASP* 1.3 74.1 - - - +
35B LEU* 1.3 64.4 + - - +
37B GLY* 3.3 2.5 + - - -
38B ALA* 3.0 22.7 + - - +
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Residues in contact with LEU 35 (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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3B TRP* 3.7 29.2 - - + +
5B LEU* 3.8 24.9 - - + -
18B VAL* 3.7 39.7 - - + -
20B VAL* 4.0 8.0 - - - +
31B ALA 3.0 13.4 + - - +
32B LEU* 3.2 15.5 + - + +
34B ALA* 1.3 75.9 - - - +
36B VAL* 1.3 57.9 + - + +
38B ALA* 3.1 6.5 + - - +
39B HIS* 3.0 24.9 + - + +
42B LEU* 3.8 19.7 - - + -
80B LEU* 4.0 16.4 - - + -
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Residues in contact with VAL 36 (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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32B LEU* 3.0 21.9 + - + +
33B ASP* 3.9 4.9 - - - +
35B LEU* 1.3 73.9 - - + +
37B GLY* 1.3 66.6 + - - +
39B HIS 3.0 5.1 - - - +
40B PRO* 2.9 33.2 - - + +
42B LEU* 4.2 16.8 - - + -
43B GLU* 3.7 40.6 - - + +
46B VAL* 4.4 11.4 - - + -
47B PHE* 3.9 22.7 - - + -
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Residues in contact with GLY 37 (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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33B ASP 2.9 16.3 + - - -
34B ALA* 3.3 4.0 + - - -
35B LEU 3.3 0.4 - - - -
36B VAL* 1.3 76.7 - - - +
38B ALA* 1.3 60.2 + - - +
40B PRO* 3.5 14.6 - - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.7 8.1 - - + -
19B ARG 5.5 1.6 - - - +
20B VAL* 5.2 3.4 - - + -
34B ALA 3.0 13.4 + - - +
35B LEU* 3.1 11.6 + - - +
37B GLY* 1.3 76.7 - - - +
39B HIS* 1.3 81.3 + - + +
40B PRO* 3.6 4.5 - - - +
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Residues in contact with HIS 39 (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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12B VAL 5.1 1.9 + - - +
13B ALA* 3.5 35.2 + - + -
15B SER* 6.5 0.4 - - - -
18B VAL* 4.0 32.9 - - + +
35B LEU* 3.0 8.2 + - + +
36B VAL 3.0 5.2 - - - +
38B ALA* 1.3 96.6 + - + +
40B PRO* 1.3 59.7 - - - +
41B ALA* 3.1 5.4 - - + +
42B LEU* 2.9 44.2 + - + +
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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