Contacts of the helix formed by residues 29 - 44 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B PRO 3.4 5.8 + - - -
28B HIS* 1.3 74.7 + - - +
30B GLU* 1.3 62.9 + - - +
31B LEU 2.9 1.3 + - - -
32B GLN* 3.0 28.8 + - - +
64B ARG 5.6 0.9 - - - -
65B TYR* 3.8 11.3 - - - -
66B SER 6.2 1.3 - - - -
70B GLU* 5.2 3.7 + - - -
276B PHE* 3.7 16.4 - - - -
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 3.0 19.5 + - + +
29B GLY* 1.3 75.7 - - - +
31B LEU* 1.3 61.7 + - - +
33B TYR* 3.1 8.2 + - + +
34B LEU* 3.1 26.2 + - + +
65B TYR* 5.1 1.3 - - - -
74B LEU* 3.3 28.1 - - + +
75B THR* 2.8 45.2 + - - +
76B THR* 2.9 31.9 + - - +
273B PRO* 4.0 10.9 - - + +
276B PHE* 3.3 19.4 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PRO* 3.9 22.7 - - + -
28B HIS* 2.9 29.1 + - + +
29B GLY 2.9 0.6 + - - -
30B GLU* 1.3 76.3 - - - +
32B GLN* 1.3 57.0 + - - +
34B LEU* 3.8 12.5 - - + +
35B GLY* 2.7 32.4 + - - -
273B PRO* 4.3 24.0 - - + -
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Residues in contact with GLN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLY* 3.0 18.6 + - - +
31B LEU* 1.3 79.2 - - - +
33B TYR* 1.3 64.1 + - - +
35B GLY* 3.8 0.5 - - - -
36B GLN* 3.1 29.2 + - - +
62B GLN 4.9 1.6 + - - -
63B ALA* 3.9 10.8 - - + +
64B ARG* 3.2 47.0 + - - +
65B TYR* 3.7 14.8 - - + +
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Residues in contact with TYR 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 4.3 0.2 + - - -
30B GLU* 3.1 10.8 + - + +
32B GLN* 1.3 80.5 - - - +
34B LEU* 1.3 78.4 + - + +
36B GLN* 3.1 18.4 + - - +
37B ILE* 3.2 39.2 + - + +
65B TYR* 3.3 18.6 + - + +
74B LEU* 3.7 27.8 - - + -
76B THR* 4.9 0.9 - - - -
77B LYS* 5.2 0.9 - - - -
219B MET* 2.6 33.2 + - + -
220B GLY* 3.7 4.9 + - - -
223B VAL* 4.1 19.1 - - + -
224B PRO* 3.2 31.7 - - + +
227B ILE* 5.3 1.6 - - + -
265B LEU* 4.8 1.9 - - - +
268B GLN* 4.2 19.2 + - - -
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Residues in contact with LEU 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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30B GLU* 3.1 14.4 + - + +
31B LEU* 3.9 14.6 - - + +
33B TYR* 1.3 91.0 - - + +
35B GLY* 1.3 64.0 + - - +
37B ILE* 3.0 17.4 + - + +
38B GLN* 3.0 11.8 + - - +
76B THR* 3.8 27.1 - - + +
268B GLN* 4.6 12.1 - - + +
269B LEU* 3.6 32.3 - - + +
271B ARG 4.6 4.9 - - - +
273B PRO* 3.8 30.1 - - + -
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Residues in contact with GLY 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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31B LEU 2.7 22.3 + - - -
32B GLN 3.8 1.1 - - - -
34B LEU* 1.3 72.6 - - - +
36B GLN* 1.3 60.8 + - - +
38B GLN* 3.0 14.3 + - - +
39B HIS* 2.9 22.8 + - - +
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Residues in contact with GLN 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN 3.1 17.6 + - - +
33B TYR* 3.1 10.5 + - - +
35B GLY* 1.3 74.8 - - - +
37B ILE* 1.3 57.6 + - - +
39B HIS* 3.4 3.9 + - - +
40B ILE* 3.0 35.2 + - - +
61B MET* 3.5 45.9 - - + +
62B GLN* 3.6 24.0 + - - +
63B ALA* 3.7 19.5 - - + +
65B TYR* 4.1 6.8 + - - -
219B MET* 3.8 17.4 - - + +
223B VAL* 5.4 1.7 - - - +
250B HIS* 5.0 7.5 + - - -
252B LEU* 5.1 7.1 - - - +
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 3.2 50.7 - - + +
34B LEU* 3.0 12.7 + - + +
36B GLN* 1.3 74.9 - - - +
38B GLN* 1.3 66.7 + - - +
40B ILE* 3.5 0.4 + - - -
41B LEU* 3.0 26.5 + - + +
219B MET* 3.8 20.9 - - + +
257B ILE* 3.5 22.2 - - + +
265B LEU* 4.1 29.4 - - + -
268B GLN* 5.4 0.4 - - - +
269B LEU* 4.3 21.8 - - + -
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Residues in contact with GLN 38 (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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34B LEU 3.0 9.7 + - - +
35B GLY* 3.0 14.8 + - - +
37B ILE* 1.3 76.9 - - - +
39B HIS* 1.3 57.7 + - - +
41B LEU* 3.2 9.1 + - + +
42B ARG* 2.9 30.7 + - + +
269B LEU* 4.2 33.1 + - + +
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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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64A ARG* 6.3 0.4 - - - -
35B GLY 2.9 12.8 + - - +
36B GLN* 3.5 12.6 - - - +
38B GLN* 1.3 72.6 - - - +
40B ILE* 1.3 59.2 + - - +
41B LEU 3.0 1.3 - - - -
42B ARG* 2.8 32.6 + - - +
43B CYS* 2.7 51.5 + - + +
58B VAL* 4.2 21.4 - - + +
61B MET* 4.1 15.5 - - + +
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Residues in contact with ILE 40 (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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36B GLN 3.0 21.7 + - - +
39B HIS* 1.3 75.4 - - - +
41B LEU* 1.3 57.3 + - - +
44B GLY* 2.8 29.6 + - - +
56B LEU* 3.6 29.0 - - + +
57B SER* 4.7 0.4 - - - -
58B VAL* 4.2 11.0 - - + -
61B MET* 3.9 17.0 - - + -
219B MET* 3.4 35.2 - - + -
255B ALA* 3.8 25.6 - - + +
257B ILE* 3.3 28.3 - - + +
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Residues in contact with LEU 41 (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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37B ILE* 3.0 24.3 + - + +
38B GLN* 3.5 6.7 - - - +
39B HIS 3.0 0.8 - - - -
40B ILE* 1.3 81.7 - - - +
42B ARG* 1.3 59.9 + - - +
43B CYS 3.6 0.3 + - - -
44B GLY 4.6 1.7 + - - +
56B LEU* 4.0 17.5 - - + +
257B ILE* 3.4 18.4 - - + -
262B ILE* 3.2 40.6 - - + +
265B LEU* 5.5 2.5 - - + -
266B LYS* 4.2 24.9 - - + +
269B LEU* 4.1 23.8 - - + -
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Residues in contact with ARG 42 (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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38B GLN* 2.9 14.5 + - + +
39B HIS* 2.8 35.6 + - - +
41B LEU* 1.3 77.1 - - - +
43B CYS* 1.3 81.6 + - - +
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Residues in contact with CYS 43 (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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39B HIS* 2.7 34.1 + - + +
41B LEU 3.3 0.2 - - - -
42B ARG* 1.3 119.2 - - - +
44B GLY* 1.3 66.6 + - - +
45B VAL* 3.3 13.9 + - - +
58B VAL* 4.2 5.0 - - + +
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Residues in contact with GLY 44 (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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40B ILE 2.8 28.0 + - - -
41B LEU 4.5 1.6 - - - +
43B CYS* 1.3 73.1 - - - +
45B VAL* 1.3 61.7 + - - +
56B LEU* 3.3 20.3 - - - +
57B SER 3.1 23.6 - - - -
58B VAL* 3.6 7.5 - - - +
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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