Contacts of the helix formed by residues 26 - 43 (chain B) in PDB entry 2G33
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 SER 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE 3.8 0.8 + - - -
25B PRO* 1.3 72.3 - - - +
27B VAL* 1.3 67.7 + - - +
28B ARG* 4.0 8.5 - - - +
29B ASP* 2.7 53.7 + - - +
30B LEU 2.9 9.2 + - - -
98B ARG* 3.5 13.3 - - - +
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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
----------------------------------------------------------
25B PRO 3.1 2.6 + - - -
26B SER* 1.3 69.3 - - - +
28B ARG* 1.3 58.3 + - - +
30B LEU* 2.7 31.1 + - + +
31B LEU* 2.8 25.9 + - + -
62B TRP* 4.0 36.3 - - + -
66B MET* 6.0 0.2 - - - -
90B ASN* 5.7 4.7 - - + +
94B GLY* 4.3 16.6 - - - +
97B PHE* 5.7 4.7 - - + -
98B ARG* 3.4 31.8 - - + +
101B LEU* 5.5 5.6 - - + -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER* 4.0 9.4 - - - +
27B VAL* 1.3 77.6 - - - +
29B ASP* 1.3 61.5 + - - +
31B LEU* 3.4 36.7 + - - +
32B ASP* 2.4 65.7 + - - +
66B MET* 4.9 19.0 - - - -
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO* 4.4 4.0 - - + +
26B SER* 2.7 44.8 + - - +
28B ARG* 1.3 77.9 - - - +
30B LEU* 1.3 48.2 + - - +
32B ASP* 3.3 5.8 - - - +
33B THR* 2.6 40.9 + - - -
127C ARG* 3.1 48.6 + - + +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO* 2.6 53.8 - - + +
26B SER 2.9 15.0 + - - +
27B VAL* 2.7 15.8 + - - +
29B ASP* 1.3 68.8 - - - +
31B LEU* 1.3 68.6 + - - +
33B THR* 3.1 8.4 - - - -
34B ALA* 2.8 24.8 + - - +
98B ARG* 4.0 11.2 - - + +
101B LEU* 3.6 25.1 - - + -
102B TRP* 3.3 43.1 - - + +
105B ILE* 3.7 7.7 - - + +
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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
----------------------------------------------------------
1A MET* 6.1 4.5 - - + -
27B VAL* 2.8 24.8 + - + +
28B ARG* 3.4 39.9 - - - +
30B LEU* 1.3 72.6 - - - +
32B ASP* 1.3 75.2 + - - +
34B ALA* 3.0 9.5 + - - +
35B ALA* 3.2 15.3 + - - +
59B ILE* 4.7 24.5 - - + -
62B TRP* 4.1 29.8 - - + +
66B MET* 4.9 4.7 - - - -
101B LEU* 4.4 17.0 - - + -
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 2.4 63.4 + - - +
29B ASP* 3.3 9.3 + - - +
31B LEU* 1.3 83.5 - - - +
33B THR* 1.3 64.8 + - - +
35B ALA* 3.9 2.6 - - - +
36B ALA* 3.0 24.8 + - - +
18C PHE* 4.5 2.0 - - + -
127C ARG* 3.7 21.5 + - - +
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Residues in contact with THR 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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25B PRO* 6.0 0.2 - - - +
29B ASP 2.6 26.2 + - - -
30B LEU* 3.1 13.5 - - - -
32B ASP* 1.3 73.4 - - - +
34B ALA* 1.3 71.5 + - - +
36B ALA* 3.1 8.3 + - - +
37B LEU* 3.2 19.7 + - + +
105B ILE* 4.7 14.4 - - + -
18C PHE* 3.3 25.9 - - + -
124C VAL* 5.0 17.5 - - + -
127C ARG* 3.3 21.0 - - - +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU 2.8 16.2 + - - +
31B LEU* 3.0 6.1 + - - +
33B THR* 1.3 79.4 - - - +
35B ALA* 1.3 55.5 + - + +
36B ALA 2.6 0.2 + - - -
37B LEU* 2.4 36.0 + - - +
38B TYR* 3.1 20.9 + - + -
42B LEU* 5.2 0.2 - - - -
55B LEU* 5.7 7.0 - - + -
59B ILE* 6.5 1.3 - - + -
101B LEU* 5.6 1.1 - - + -
105B ILE* 4.1 25.1 - - + -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.2 42.0 - - + -
31B LEU 3.2 9.9 + - - +
32B ASP* 4.4 1.6 - - - +
34B ALA* 1.3 77.6 - - - +
36B ALA* 1.3 55.7 + - - +
37B LEU 3.1 1.3 - - - -
39B ARG* 2.8 41.5 + - + +
42B LEU* 4.4 10.0 - - + +
14C GLU* 3.5 8.6 - - - +
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Residues in contact with ALA 36 (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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32B ASP* 3.0 19.1 + - - +
33B THR 3.4 4.9 - - - +
34B ALA 2.6 4.0 + - - -
35B ALA* 1.3 75.2 - - - +
37B LEU* 1.3 60.0 + - - +
39B ARG* 4.9 0.7 - - - -
12C THR* 5.2 4.2 - - - +
14C GLU* 4.0 28.9 - - + +
15C LEU* 4.7 19.2 - - - +
18C PHE* 3.9 22.8 - - + -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 3.5 16.4 - - + +
34B ALA* 2.4 25.8 + - - +
36B ALA* 1.3 73.0 - - - +
38B TYR* 1.3 100.6 + - + +
105B ILE* 6.0 2.5 - - + -
109B THR* 5.1 7.2 - - + +
18C PHE* 6.2 0.4 - - + -
120C VAL* 3.9 33.0 - - + -
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Residues in contact with TYR 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 ALA* 3.1 18.6 + - + +
36B ALA 3.6 0.2 - - - -
37B LEU* 1.3 124.2 - - + +
39B ARG* 1.3 53.1 + - - +
40B ASP* 3.3 2.5 - - - -
41B ALA* 2.4 50.1 + - + +
42B LEU* 3.3 25.2 + - + -
52B HIS* 6.0 1.3 - - + -
105B ILE* 4.5 15.0 - - + -
108B LEU* 2.7 49.0 + - + -
109B THR* 2.9 19.1 + - - +
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Residues in contact with ARG 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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1A MET* 2.8 51.5 - - - +
2A ASP 4.4 1.6 - - - +
35B ALA* 2.8 19.0 + - - +
36B ALA 5.5 0.2 - - - -
38B TYR* 1.3 75.7 - - - +
40B ASP* 1.3 59.3 + - - +
42B LEU* 2.5 36.5 + - - +
43B GLU* 3.0 45.5 + - + +
14C GLU* 2.8 52.7 + - - +
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Residues in contact with ASP 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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38B TYR 2.8 3.2 + - - +
39B ARG* 1.3 80.5 - - - +
41B ALA* 1.3 60.9 + - - +
42B LEU 3.2 0.5 + - - -
43B GLU* 3.8 12.2 + - - +
44B SER* 3.4 18.5 + - - -
12C THR* 6.1 1.4 - - - +
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Residues in contact with ALA 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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38B TYR* 2.4 41.4 + - + +
40B ASP* 1.3 70.5 - - - +
42B LEU* 1.3 60.4 + - + +
44B SER* 3.2 14.9 + - - -
46B GLU 4.7 2.3 - - - +
52B HIS* 4.7 11.2 - - + +
56B ARG* 3.0 15.6 + - - -
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Residues in contact with LEU 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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1A MET* 6.3 1.6 - - - -
3A ILE* 5.4 9.6 - - + +
4A ASP 5.6 1.9 - - - +
7A LYS* 5.8 0.3 - - - +
34B ALA* 5.2 1.6 - - + -
35B ALA* 4.4 14.8 - - + +
38B TYR* 3.5 34.5 - - + +
39B ARG* 2.5 25.6 + - - +
41B ALA* 1.3 78.6 - - - +
43B GLU* 1.3 56.0 + - + +
44B SER 2.5 27.2 + - - +
52B HIS* 4.3 14.8 - - + -
55B LEU* 4.7 20.9 - - + -
56B ARG* 3.3 36.1 + - + +
108B LEU* 6.1 0.9 - - + -
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Residues in contact with GLU 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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2A ASP* 2.7 32.9 + - - +
3A ILE* 3.7 17.3 - - + +
4A ASP 5.9 0.2 - - - +
7A LYS* 3.4 35.9 + - - +
39B ARG* 3.0 52.0 + - + +
40B ASP* 4.1 11.9 - - - +
42B LEU* 1.3 73.0 - - + +
44B SER* 1.3 55.1 + - - +
45B PRO* 4.1 2.4 - - - +
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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
------------------------------------------------------------
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