Contacts of the helix formed by residues 29 - 44 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A PRO 3.4 3.6 + - - -
28A HIS* 1.3 72.5 + - - +
30A GLU* 1.3 58.0 + - - +
31A LEU 3.0 10.4 + - - -
32A GLN* 3.2 18.6 + - - +
64A ARG 5.6 2.9 - - - -
65A TYR* 3.5 22.7 - - - -
66A SER 6.2 0.9 - - - -
70A GLU* 5.1 4.5 + - - -
276A PHE* 4.0 16.0 - - - -
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A HIS* 2.8 26.7 + - + +
29A GLY* 1.3 71.1 - - - -
31A LEU* 1.3 61.7 + - - +
32A GLN 3.2 0.4 - - - -
33A TYR* 3.2 8.8 + - + +
34A LEU* 3.0 29.9 + - + +
65A TYR* 4.7 0.7 - - - -
74A LEU* 3.3 28.4 - - + +
75A THR* 2.5 34.9 + - - -
76A THR* 2.7 42.0 + - - -
273A PRO* 4.0 6.5 - - + -
276A PHE* 3.7 14.2 - - + -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PRO* 3.9 27.8 - - + -
28A HIS* 3.3 23.5 + - + +
29A GLY 3.0 0.8 - - - -
30A GLU* 1.3 76.7 - - - +
32A GLN* 1.3 56.8 + - + +
34A LEU* 3.7 13.1 - - + +
35A GLY* 2.8 30.7 + - - -
273A PRO* 4.0 23.6 - - + -
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Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A HIS 5.8 0.2 - - - +
29A GLY* 3.2 15.9 + - - +
31A LEU* 1.3 73.4 - - + +
33A TYR* 1.3 69.0 + - - +
35A GLY* 3.1 2.8 + - - -
36A GLN* 2.9 28.1 + - + +
62A GLN 4.3 2.9 - - - +
63A ALA* 3.5 18.3 - - + -
64A ARG* 2.7 50.0 + - - +
65A TYR* 4.4 2.0 - - + -
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Residues in contact with TYR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLY 4.2 0.2 + - - -
30A GLU* 3.2 14.3 + - + +
32A GLN* 1.3 77.9 - - - +
34A LEU* 1.3 84.6 + - + +
36A GLN* 2.8 22.9 + - - +
37A ILE* 3.1 30.2 + - + +
65A TYR* 3.2 24.4 + - + +
74A LEU* 3.5 35.2 - - + +
76A THR* 4.5 2.0 - - - -
77A LYS* 6.2 0.2 - - - +
219A MET* 2.6 49.6 + - + -
220A GLY* 4.1 5.5 + - - -
223A VAL* 4.2 10.1 - - + -
224A PRO* 3.3 18.6 - - + +
227A ILE* 4.4 1.6 - - + -
268A GLN* 4.1 20.8 + - - -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLU* 3.0 19.7 + - + +
31A LEU* 3.8 15.9 - - + +
33A TYR* 1.3 88.8 - - + +
35A GLY* 1.3 61.9 + - - +
37A ILE* 3.2 5.7 + - - +
38A GLN* 2.9 21.9 + - - +
76A THR* 3.8 30.5 - - + +
268A GLN* 4.5 10.5 - - - +
269A LEU* 3.5 34.1 - - + +
271A ARG 4.3 8.5 - - - +
273A PRO* 3.7 29.8 - - + -
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU 2.8 20.1 + - - -
32A GLN* 3.1 4.5 + - - -
34A LEU* 1.3 73.2 - - - +
36A GLN* 1.3 56.7 + - - +
38A GLN* 3.1 10.2 + - - +
39A HIS* 2.8 29.9 + - - +
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Residues in contact with GLN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 2.9 15.3 + - + +
33A TYR* 2.8 19.2 + - - +
35A GLY* 1.3 75.7 - - - +
37A ILE* 1.3 62.5 + - - +
39A HIS* 3.3 4.3 + - - +
40A ILE* 3.0 26.8 + - - +
61A MET* 3.5 46.6 - - + +
62A GLN* 3.6 25.0 + - - +
63A ALA* 3.8 17.0 - - + +
65A TYR* 3.9 3.1 + - - -
219A MET* 3.8 22.5 - - + +
223A VAL* 5.4 0.9 - - - +
250A HIS* 4.8 6.7 + - - -
252A LEU* 4.8 6.8 - - - +
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TYR* 3.1 45.3 + - + +
34A LEU* 3.4 8.5 - - + +
36A GLN* 1.3 73.5 - - - +
38A GLN* 1.3 65.2 + - - +
40A ILE* 2.8 22.7 + - - +
41A LEU* 3.1 13.9 + - + +
219A MET* 4.1 23.8 - - + +
257A ILE* 3.7 18.4 - - + -
265A LEU* 3.6 25.6 - - + -
268A GLN* 4.9 1.6 - - - +
269A LEU* 3.4 33.2 - - + -
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Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU 2.9 15.6 + - - +
35A GLY* 3.1 13.4 + - - +
37A ILE* 1.3 76.8 - - - +
39A HIS* 1.3 57.8 - - - +
41A LEU* 3.4 13.5 + - - +
42A ARG* 3.0 32.9 + - - +
266A LYS* 5.5 3.0 - - - +
269A LEU* 3.1 34.8 - - + +
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Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLY 2.8 13.1 + - - +
36A GLN* 3.4 9.6 - - - +
37A ILE 3.0 0.4 + - - -
38A GLN* 1.3 73.2 - - - +
40A ILE* 1.3 61.4 + - - +
42A ARG* 3.3 29.5 + - - +
43A CYS* 2.9 53.7 + - + +
44A GLY 3.6 0.3 + - - -
58A VAL* 4.2 16.2 - - + +
61A MET* 3.5 24.9 - - + -
64B ARG* 5.9 4.2 + - - -
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN 3.0 17.0 + - - +
37A ILE* 2.8 12.0 + - - +
39A HIS* 1.3 75.6 - - - +
41A LEU* 1.3 59.6 + - - +
44A GLY* 2.5 32.7 + - - -
56A LEU* 3.2 40.8 - - + +
57A SER* 4.2 2.2 - - - -
58A VAL* 3.5 28.7 - - + -
61A MET* 3.6 12.1 - - - -
219A MET* 4.5 10.5 - - + -
255A ALA* 3.1 28.0 - - + +
257A ILE* 4.4 15.0 - - + -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.1 14.6 + - + +
38A GLN* 3.6 15.7 - - - +
40A ILE* 1.3 79.5 - - + +
42A ARG* 1.3 63.4 + - - +
44A GLY 4.2 3.8 + - - +
56A LEU* 3.7 22.8 - - + +
257A ILE* 5.0 10.3 - - + -
262A ILE* 4.1 33.2 - - + +
265A LEU* 5.8 1.6 - - + -
266A LYS* 4.4 16.2 - - + +
269A LEU* 3.6 31.4 - - + -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 3.0 12.9 + - - +
39A HIS* 3.3 41.6 + - - +
41A LEU* 1.3 80.8 - - - +
43A CYS* 1.3 75.2 + - - +
44A GLY 4.9 0.9 - - - +
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Residues in contact with CYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A HIS* 2.9 30.3 + - + +
42A ARG* 1.3 116.6 - - - +
44A GLY* 1.3 68.0 + - - +
45A VAL* 4.1 7.6 - - - +
58A VAL* 4.6 3.2 - - + +
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A HIS 3.6 0.8 + - - -
40A ILE 2.5 28.8 + - - -
41A LEU 4.8 3.3 - - - +
42A ARG 3.7 1.8 - - - +
43A CYS* 1.3 78.5 - - - +
45A VAL* 1.3 62.6 + - - +
56A LEU* 4.0 11.8 - - - +
57A SER 3.5 15.3 - - - -
58A VAL* 3.9 7.8 - - - +
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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