Contacts of the helix formed by residues 23 - 35 (chain B) in PDB entry 3G33
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 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B ASP* 1.3 66.0 + - - -
25B GLN* 3.3 3.6 - - - +
26B ARG* 3.7 38.1 + - - +
27B VAL* 3.4 17.8 + - - +
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Residues in contact with ASP 24 (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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23B GLY* 1.3 72.5 - - - +
25B GLN* 1.3 66.9 + - + +
26B ARG 3.2 0.4 - - - -
27B VAL* 3.1 17.9 + - - +
28B LEU* 3.1 20.8 + - + +
163B PHE* 4.0 27.5 - - + -
166B HIS* 4.7 21.0 + - - +
167B ARG* 5.4 2.2 - - - +
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Residues in contact with GLN 25 (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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23B GLY 3.3 2.0 - - - +
24B ASP* 1.3 80.8 - - + +
26B ARG* 1.3 62.8 + - + +
28B LEU* 3.7 3.3 + - - +
29B GLN* 3.4 31.6 + - - +
167B ARG* 3.3 31.8 - - - +
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Residues in contact with ARG 26 (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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23B GLY 3.7 28.1 + - - +
24B ASP 3.2 0.6 - - - -
25B GLN* 1.3 78.3 - - + +
27B VAL* 1.3 62.9 + - + +
29B GLN* 3.9 14.1 + - - +
30B SER* 3.3 18.9 + - - -
292C PHE* 5.1 18.3 - - - -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY 3.4 19.1 - - - +
24B ASP* 3.1 11.6 + - - +
26B ARG* 1.3 77.4 - - + +
28B LEU* 1.3 64.9 + - - +
30B SER* 2.6 22.9 + - - +
31B LEU* 3.0 21.3 + - + +
163B PHE* 3.5 34.1 - - + -
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Residues in contact with LEU 28 (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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24B ASP* 3.1 17.9 + - + +
25B GLN* 4.0 5.4 - - - +
26B ARG 3.5 0.2 - - - -
27B VAL* 1.3 77.2 - - - +
29B GLN* 1.3 63.0 + - + +
31B LEU* 3.2 6.8 + - + +
32B LEU* 2.9 38.0 + - + +
160B PHE* 4.3 26.0 - - + -
163B PHE* 4.2 29.4 - - + +
164B ILE* 4.9 2.9 - - + -
167B ARG* 3.8 40.2 - - + +
232B ILE* 4.3 22.2 - - + +
233B THR* 5.2 3.6 - - + -
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Residues in contact with GLN 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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25B GLN* 3.4 20.7 + - - +
26B ARG* 4.1 13.6 - - - +
27B VAL 3.4 0.4 - - - -
28B LEU* 1.3 76.7 - - + +
30B SER* 1.3 62.9 + - - +
32B LEU* 3.7 11.0 - - + +
33B ARG* 3.1 28.2 + - + +
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Residues in contact with SER 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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26B ARG 3.3 13.0 + - - -
27B VAL* 2.6 26.3 + - - +
29B GLN* 1.3 75.7 - - - +
31B LEU* 1.3 67.2 + - - +
33B ARG* 3.1 20.9 + - - +
34B LEU* 3.1 18.5 + - - +
71C PHE* 4.0 23.5 - - - -
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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
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27B VAL* 3.0 29.8 + - + +
28B LEU* 3.6 7.2 - - + +
30B SER* 1.3 77.0 + - - +
32B LEU* 1.3 64.2 + - - +
34B LEU* 3.0 17.7 + - + +
35B GLU* 3.4 13.6 + - - +
155B VAL* 4.0 28.9 - - + +
159B ASP* 3.8 28.3 - - + +
160B PHE* 4.0 22.0 - - + -
163B PHE* 3.8 23.1 - - + -
67C ARG* 4.0 14.8 - - - +
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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
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28B LEU* 2.9 30.7 + - + +
29B GLN* 3.7 9.4 - - + +
31B LEU* 1.3 75.3 - - - +
33B ARG* 1.3 65.7 + - + +
35B GLU* 3.0 45.1 + - - +
36B GLU* 4.7 2.9 + - - +
160B PHE* 3.9 10.5 - - + -
201B SER* 3.9 17.3 - - - +
232B ILE 4.9 3.1 - - - +
233B THR* 3.7 36.3 - - + +
234B GLY* 5.6 0.7 - - - -
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Residues in contact with ARG 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 GLN* 3.1 15.8 + - + +
30B SER* 3.1 16.7 + - - +
32B LEU* 1.3 80.9 - - - +
34B LEU* 1.3 65.9 + - + +
35B GLU 3.5 0.2 + - - -
36B GLU* 4.1 19.3 + - - +
71C PHE* 4.9 26.1 + - + +
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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 SER* 3.4 15.5 - - - +
31B LEU* 3.0 9.5 + - + +
33B ARG* 1.3 77.7 - - + +
35B GLU* 1.3 67.9 + - - +
36B GLU 3.1 2.5 - - - -
37B ARG* 2.7 25.2 + - - +
38B TYR* 3.8 11.1 + - + -
155B VAL* 3.9 12.1 - - + -
67C ARG* 3.4 43.1 - - + +
70C ALA* 3.8 29.2 - - + -
71C PHE* 3.7 36.1 - - + +
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Residues in contact with GLU 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 3.4 10.0 + - - +
32B LEU* 3.0 43.6 + - - +
34B LEU* 1.3 76.6 - - - +
36B GLU* 1.3 66.1 + - + +
38B TYR* 2.9 16.1 + - - +
39B VAL* 3.0 16.3 + - + +
155B VAL* 4.6 8.5 - - + -
160B PHE* 3.8 11.0 - - + -
199B PRO* 3.9 6.9 - - + +
200B PRO* 3.4 24.7 - - + +
201B SER* 2.7 42.7 + - - -
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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