Contacts of the helix formed by residues 29 - 42 (chain E) in PDB entry 3HB8
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 GLY 29 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E PRO 3.4 6.0 + - - -
28E HIS* 1.3 72.8 + - - +
30E GLU* 1.3 60.1 + - - +
31E LEU 3.1 0.2 - - - -
32E GLN* 3.3 27.9 + - - +
64E ARG 5.2 4.0 - - - -
65E TYR* 3.5 19.4 - - - -
66E SER 6.0 1.3 - - - -
70E GLU* 5.4 2.6 + - - -
276E PHE* 4.0 16.6 - - - -
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Residues in contact with GLU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E HIS* 2.7 27.8 + - + +
29E GLY* 1.3 71.7 - - - +
31E LEU* 1.3 62.2 + - - +
32E GLN 3.1 0.2 - - - -
33E TYR* 3.0 7.9 + - + +
34E LEU* 3.0 29.8 + - + +
74E LEU* 3.3 30.1 - - + +
75E THR* 2.8 35.6 + - - +
76E THR* 2.8 36.1 + - - -
273E PRO* 3.5 15.7 - - + +
276E PHE* 3.7 9.4 - - + -
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Residues in contact with LEU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E PRO* 3.7 17.0 - - + -
28E HIS* 2.7 45.3 + - + +
30E GLU* 1.3 73.2 - - - +
32E GLN* 1.3 52.4 + - + +
34E LEU* 3.3 11.9 + - + +
35E GLY* 2.7 34.3 + - - -
273E PRO* 4.3 20.2 - - + -
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Residues in contact with GLN 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E HIS 5.3 0.2 - - - +
29E GLY* 3.4 15.9 - - - +
30E GLU 3.1 0.6 - - - -
31E LEU* 1.3 80.0 - - + +
33E TYR* 1.3 63.1 + - - +
35E GLY* 3.4 1.9 + - - -
36E GLN* 3.1 29.2 + - + +
63E ALA* 3.3 16.0 - - + +
64E ARG* 2.7 54.8 + - - +
65E TYR* 4.4 3.7 - - + -
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Residues in contact with TYR 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E GLY 4.0 0.6 + - - -
30E GLU* 3.0 13.5 + - + +
32E GLN* 1.3 79.8 - - - +
34E LEU* 1.3 85.3 + - + +
36E GLN* 3.1 18.7 + - - +
37E ILE* 3.3 34.6 + - + +
65E TYR* 3.5 22.7 + - + +
74E LEU* 3.8 24.2 - - + -
76E THR* 5.0 0.4 - - - -
77E LYS* 6.0 0.5 - - - +
219E MET* 2.5 32.5 + - + -
220E GLY* 4.2 3.8 + - - -
223E VAL* 4.0 18.6 - - + -
224E PRO* 3.4 30.2 - - + +
227E ILE* 4.2 2.9 - - + -
265E LEU* 4.7 5.6 - - + +
268E GLN* 4.3 16.3 + - - -
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Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E GLU* 3.0 19.9 + - + +
31E LEU* 3.7 16.6 - - + +
33E TYR* 1.3 92.8 - - + +
35E GLY* 1.3 63.9 + - - +
37E ILE* 2.8 17.1 + - + +
38E GLN* 3.1 11.6 + - - +
76E THR* 3.8 30.3 - - + +
268E GLN* 4.6 10.3 - - + +
269E LEU* 3.8 32.4 - - + +
271E ARG 4.4 6.7 - - - +
273E PRO* 4.2 25.4 - - + -
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Residues in contact with GLY 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU 2.7 21.4 + - - -
32E GLN* 3.8 2.2 - - - -
34E LEU* 1.3 72.7 - - - +
36E GLN* 1.3 60.8 + - - +
38E GLN* 3.0 41.7 + - - +
39E HIS* 3.1 9.8 + - - +
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Residues in contact with GLN 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E GLN 3.1 17.0 + - - +
33E TYR* 3.3 18.6 - - - +
34E LEU 3.1 0.2 - - - -
35E GLY* 1.3 76.1 - - - +
37E ILE* 1.3 58.1 + - - +
39E HIS* 3.3 3.4 + - - +
40E ILE* 2.8 35.2 + - - +
61E MET* 3.4 46.2 - - + +
62E GLN 3.8 12.7 + - - +
63E ALA* 4.0 21.5 - - + +
65E TYR* 4.0 3.3 + - - -
219E MET* 3.6 23.4 - - + +
223E VAL* 5.4 0.7 - - - +
250E HIS* 5.0 1.9 + - - -
252E LEU* 4.2 12.2 - - - +
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Residues in contact with ILE 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E TYR* 3.3 35.7 + - + +
34E LEU* 2.8 10.9 + - + +
36E GLN* 1.3 76.2 - - - +
38E GLN* 1.3 65.6 + - - +
40E ILE* 3.1 13.1 + - - +
41E LEU* 3.2 18.0 + - + +
219E MET* 3.3 39.9 - - + -
257E ILE* 3.6 23.5 - - + +
265E LEU* 4.2 22.2 - - + -
269E LEU* 3.8 29.8 - - + -
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Residues in contact with GLN 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU 3.1 5.7 + - - +
35E GLY* 3.0 31.2 + - - +
37E ILE* 1.3 82.9 - - - +
39E HIS* 1.3 65.7 + - - +
41E LEU* 3.3 11.6 + - + +
42E ARG* 3.1 42.8 + - + +
269E LEU* 4.3 15.3 - - + -
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Residues in contact with HIS 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ARG* 6.1 0.4 + - - -
35E GLY 3.1 10.6 + - - +
36E GLN* 3.4 9.6 - - - +
38E GLN* 1.3 79.8 - - + +
40E ILE* 1.3 65.8 + - - +
41E LEU 3.0 3.5 + - - -
42E ARG* 4.6 8.2 - - - +
43E CYS* 3.1 55.8 + - + +
58E VAL* 4.2 19.0 - - + +
61E MET* 3.4 26.7 - - + +
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Residues in contact with ILE 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E GLN 2.8 28.1 + - - +
37E ILE* 3.1 8.5 + - - +
39E HIS* 1.3 75.5 - - - +
41E LEU* 1.3 57.1 + - - +
44E GLY* 2.8 22.4 + - - -
56E LEU* 2.9 39.0 - - + +
58E VAL* 3.6 24.0 - - + -
61E MET* 3.6 25.8 - - + -
219E MET* 4.5 7.0 - - + -
255E ALA* 3.6 18.4 - - + +
256E HIS 4.3 0.2 - - - -
257E ILE* 3.4 35.4 - - + +
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Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE* 3.2 17.9 + - + +
38E GLN* 3.4 14.4 - - - +
39E HIS 3.0 1.6 - - - -
40E ILE* 1.3 78.3 - - - +
42E ARG* 1.3 54.2 + - + +
43E CYS 2.7 16.4 + - - -
44E GLY 3.5 6.4 + - - +
56E LEU* 3.5 27.2 - - + +
257E ILE* 4.3 16.2 - - + -
262E ILE* 4.4 27.6 - - + +
265E LEU* 5.8 2.5 - - + -
266E LYS* 4.1 26.9 - - + +
269E LEU* 4.5 15.5 - - + -
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Residues in contact with ARG 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E GLN* 3.1 31.1 + - + +
39E HIS* 4.8 7.6 - - - +
41E LEU* 1.3 76.2 - - + +
43E CYS* 1.3 82.3 + - - +
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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