Contacts of the helix formed by residues 29 - 44 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C PRO 3.8 2.2 + - - -
28C HIS* 1.3 72.9 + - - +
30C GLU* 1.3 58.4 + - - +
31C LEU 2.9 10.8 + - - -
32C GLN* 3.0 33.4 + - - +
64C ARG 5.1 0.9 - - - -
65C TYR* 3.4 18.2 - - - -
66C SER 5.9 1.6 - - - -
70C GLU* 5.1 3.7 + - - -
276C PHE* 3.9 16.9 - - - -
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C HIS* 2.8 27.1 + - + +
29C GLY* 1.3 71.0 - - - -
31C LEU* 1.3 56.7 + - - +
32C GLN 3.2 0.2 - - - -
33C TYR* 3.4 6.1 + - + +
34C LEU* 2.9 32.4 + - + +
65C TYR* 4.8 0.7 - - - -
74C LEU* 3.3 27.5 - - + +
75C THR* 2.7 35.3 + - - +
76C THR* 2.5 52.6 + - + -
273C PRO* 4.3 4.0 - - + -
276C PHE* 3.7 12.0 - - + -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PRO* 4.2 11.0 - - + -
28C HIS* 3.0 44.9 + - + +
29C GLY 2.9 0.2 - - - -
30C GLU* 1.3 76.3 - - - +
32C GLN* 1.3 64.3 + - - +
34C LEU* 3.8 11.9 - - + +
35C GLY* 2.8 26.3 + - - -
273C PRO* 4.6 17.5 - - + +
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Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PRO* 5.2 10.4 - - - +
28C HIS 3.4 12.6 + - - +
29C GLY* 3.0 19.8 + - - +
31C LEU* 1.3 80.2 - - - +
33C TYR* 1.3 65.8 + - - +
35C GLY* 3.2 3.2 + - - -
36C GLN* 3.1 27.0 + - - +
63C ALA* 4.0 16.8 - - + -
64C ARG* 3.2 34.2 + - - +
65C TYR* 4.3 4.5 - - + -
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Residues in contact with TYR 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY 3.9 0.4 + - - -
30C GLU* 3.4 13.5 + - + +
32C GLN* 1.3 79.7 - - - +
34C LEU* 1.3 71.6 + - + +
36C GLN* 3.1 19.4 + - - +
37C ILE* 3.3 37.9 + - + +
65C TYR* 3.2 23.6 + - + +
74C LEU* 3.4 31.9 - - + -
76C THR* 4.5 0.2 - - - -
219C MET* 2.8 37.9 + - + -
220C GLY 3.9 3.1 + - - -
223C VAL* 3.9 23.6 - - + -
224C PRO* 3.6 20.4 - - + +
227C ILE* 4.4 1.6 - - + -
265C LEU* 4.7 2.6 - - - +
268C GLN* 3.7 21.9 + - - -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLU* 2.9 25.7 + - + +
31C LEU* 3.8 13.2 - - + +
33C TYR* 1.3 82.1 - - + +
35C GLY* 1.3 63.4 + - - +
37C ILE* 3.2 21.9 + - + -
38C GLN* 3.3 12.3 + - - +
76C THR* 3.8 24.9 - - + +
268C GLN* 4.4 4.5 - - - +
269C LEU* 3.4 46.6 - - + +
271C ARG 4.5 5.2 - - - +
273C PRO* 3.7 30.1 - - + -
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Residues in contact with GLY 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU 2.8 18.0 + - - -
32C GLN 3.2 2.4 + - - -
34C LEU* 1.3 75.8 - - - +
36C GLN* 1.3 62.0 + - - +
38C GLN* 3.4 14.6 + - - +
39C HIS* 3.0 23.6 + - - +
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Residues in contact with GLN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLN 3.1 14.0 + - - +
33C TYR* 3.1 21.5 + - - +
35C GLY* 1.3 74.3 - - - +
37C ILE* 1.3 66.0 + - - +
39C HIS* 3.3 6.7 + - - +
40C ILE* 3.0 31.0 + - - +
61C MET* 3.5 48.5 - - + +
62C GLN 3.8 21.1 + - - +
63C ALA* 3.9 16.1 - - + +
65C TYR* 4.0 3.5 + - - -
219C MET* 3.7 11.0 - - + +
223C VAL* 5.4 1.4 - - - +
250C HIS* 4.9 6.4 + - - -
252C LEU* 4.7 7.9 - - - +
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Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C TYR* 3.3 49.6 - - + +
34C LEU* 3.2 19.0 + - + +
36C GLN* 1.3 75.6 - - - +
38C GLN* 1.3 58.6 + - - +
40C ILE* 3.3 5.1 + - - +
41C LEU* 2.9 41.6 + - + +
219C MET* 3.8 18.8 - - + -
257C ILE* 3.5 21.2 - - + +
265C LEU* 3.9 28.0 - - + -
268C GLN* 4.7 1.1 - - - +
269C LEU* 3.9 13.9 - - + -
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Residues in contact with GLN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU 3.3 5.7 + - - +
35C GLY* 3.6 16.9 + - - +
36C GLN 3.3 0.2 - - - -
37C ILE* 1.3 79.0 - - - +
39C HIS* 1.3 51.9 + - - +
41C LEU* 2.7 13.2 + - + +
42C ARG* 2.7 37.4 + - - +
269C LEU* 3.5 31.1 - - + +
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Residues in contact with HIS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLY 3.0 13.9 + - - +
36C GLN* 3.6 8.7 - - - +
38C GLN* 1.3 77.6 - - - +
40C ILE* 1.3 59.8 + - + +
42C ARG* 3.1 13.1 + - - +
43C CYS* 2.6 63.3 + - + +
58C VAL* 4.1 23.9 - - + +
61C MET* 4.9 7.0 - - + -
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Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLN 3.0 18.3 + - - +
37C ILE* 3.5 5.6 - - - +
39C HIS* 1.3 74.4 - - - +
41C LEU* 1.3 58.9 + - - +
44C GLY* 2.7 28.9 + - - -
56C LEU* 3.0 38.4 - - + +
58C VAL* 3.7 26.5 - - + -
61C MET* 3.5 25.1 - - + -
219C MET* 3.4 33.4 - - + -
255C ALA 4.3 6.5 - - - +
256C HIS* 4.5 1.3 - - - -
257C ILE* 3.8 16.2 - - + +
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ILE* 2.9 20.5 + - + +
38C GLN* 2.7 17.7 + - + +
40C ILE* 1.3 73.5 - - - +
42C ARG* 1.3 56.9 + - - +
44C GLY 4.7 0.3 + - - -
56C LEU* 4.0 16.9 - - + +
257C ILE* 4.0 13.5 - - + -
262C ILE* 3.8 39.9 - - + +
265C LEU* 5.3 1.3 - - + -
266C LYS* 4.1 27.8 - - + +
269C LEU* 3.7 30.5 - - + -
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLN 2.7 18.0 + - - +
39C HIS* 3.8 13.6 + - - +
41C LEU* 1.3 77.8 - - - +
43C CYS* 1.3 85.1 + - - +
44C GLY 3.3 3.3 + - - +
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Residues in contact with CYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C HIS* 2.6 42.6 + - + +
42C ARG* 1.3 108.0 - - - +
44C GLY* 1.3 67.3 + - - +
45C VAL* 3.9 7.3 - - - +
57C SER 4.9 0.2 - - - +
58C VAL* 4.5 5.3 - - - +
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Residues in contact with GLY 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C HIS 3.5 0.2 + - - -
40C ILE* 2.7 33.6 + - - -
41C LEU 4.4 0.2 - - - -
42C ARG 3.3 4.9 + - - +
43C CYS* 1.3 83.2 - - - +
45C VAL* 1.3 65.4 + - - +
56C LEU* 4.5 8.7 - - - -
57C SER 3.9 0.7 - - - -
58C VAL* 3.7 15.9 - - - -
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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