Contacts of the helix formed by residues 37 - 46 (chain B) in PDB entry 2GAO
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 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASN 3.3 0.6 - - - -
36B ALA* 1.3 77.1 - - - +
38B LYS* 1.3 60.0 + - - +
40B THR* 3.3 3.3 + - - -
41B LEU* 3.0 29.1 + - - +
99B LEU* 3.5 7.9 - - - +
134B ASN* 3.9 3.1 - - - -
180B VAL* 4.2 2.8 - - - +
501B GDP 3.1 41.5 + - - -
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Residues in contact with LYS 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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30B PHE* 3.5 28.7 - - + +
31B LEU 3.8 3.4 - - - -
32B GLY* 3.4 29.1 + - - +
33B LEU 2.9 18.8 + - - -
36B ALA* 3.9 2.4 - - - +
37B GLY* 1.3 76.0 - - - +
39B THR* 1.3 62.4 + - - +
41B LEU* 3.6 4.1 + - - +
42B LEU* 3.0 26.2 + - - +
60B THR 5.3 1.8 - - - +
73B THR* 3.7 17.5 - - - +
74B PHE 3.5 23.8 - - - +
75B ASP* 2.7 23.9 + - - +
99B LEU* 3.7 14.7 - - + +
501B GDP 2.7 34.2 + - - +
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Residues in contact with THR 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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38B LYS* 1.3 76.2 - - - +
40B THR* 1.3 59.7 + - - +
42B LEU* 3.3 6.5 + - + +
43B HIS* 2.9 28.2 + - + +
54B VAL* 3.7 21.8 - - + -
58B HIS* 3.1 26.5 + - + -
59B PRO 4.4 2.8 + - - -
60B THR 5.5 1.4 + - - -
62B GLU* 3.7 30.8 + - - +
73B THR* 4.6 9.7 + - - -
501B GDP 2.9 23.9 + - - -
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Residues in contact with THR 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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37B GLY 3.6 5.4 - - - -
39B THR* 1.3 75.3 - - - +
41B LEU* 1.3 59.4 + - - +
43B HIS* 3.3 2.6 + - - +
44B MET* 2.9 40.4 + - + +
54B VAL* 3.9 23.1 - - + +
180B VAL* 3.7 15.5 - - + -
181B LEU* 3.8 28.0 - - + -
501B GDP 2.5 49.6 + - + +
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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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30B PHE* 3.8 21.8 - - + -
37B GLY 3.0 16.8 + - - +
38B LYS 3.7 4.3 - - - +
40B THR* 1.3 73.5 - - - +
42B LEU* 1.3 66.1 + - - +
44B MET* 3.2 10.8 + - - +
45B LEU* 3.3 16.1 + - + +
97B VAL* 4.4 1.3 - - + -
99B LEU* 3.9 20.0 - - + -
132B LEU* 3.7 26.9 - - + -
180B VAL* 3.4 14.5 - - + +
186B TYR* 3.8 43.7 - - + -
190B PHE* 4.1 14.4 - - + -
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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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30B PHE* 4.1 12.3 - - + -
38B LYS 3.0 18.2 + - - +
39B THR* 3.7 5.6 - - - +
41B LEU* 1.3 75.6 - - - +
43B HIS* 1.3 63.5 + - - +
45B LEU* 3.1 16.0 + - + +
46B LYS* 3.3 25.0 + - - +
62B GLU* 3.7 47.6 - - + +
63B GLU 4.2 2.5 - - - +
64B LEU* 3.9 17.8 - - + +
71B PHE* 3.4 40.8 - - + +
73B THR* 4.1 10.3 - - + -
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Residues in contact with HIS 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 THR* 2.9 12.2 + - + +
40B THR 3.5 2.4 + - - +
42B LEU* 1.3 76.4 - - - +
44B MET* 1.3 80.6 + - + +
46B LYS* 3.2 42.0 + - + +
54B VAL* 3.2 45.9 + - + +
183B ARG* 5.4 3.4 + - - -
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Residues in contact with MET 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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15B VAL* 4.4 7.1 - - - +
40B THR* 2.9 28.9 + - + +
41B LEU* 3.2 8.9 + - - +
43B HIS* 1.3 90.6 - - + +
45B LEU* 1.3 61.3 + - - +
46B LYS 3.5 3.2 - - - +
180B VAL* 3.7 22.0 - - + +
181B LEU* 3.6 34.3 - - + +
183B ARG* 3.5 49.9 + - - +
186B TYR* 3.4 23.5 + - + +
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Residues in contact with LEU 45 (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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15B VAL* 3.4 32.8 - - + +
18B PHE* 6.3 0.4 - - + -
19B LEU* 3.3 35.7 - - + -
30B PHE* 4.0 18.2 - - + -
41B LEU* 3.3 14.6 + - + +
42B LEU* 3.1 10.1 + - - +
44B MET* 1.3 78.5 - - - +
46B LYS* 1.3 66.5 + - - +
64B LEU* 3.9 10.5 - - + -
66B ILE* 3.6 9.3 - - + +
71B PHE* 3.9 43.5 - - + -
186B TYR* 4.8 10.8 - - + -
190B PHE* 4.9 3.6 - - + -
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Residues in contact with LYS 46 (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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61A SER* 5.7 2.8 + - - -
63A GLU* 3.5 34.6 + - - +
65A THR* 6.1 0.9 - - - -
72A THR* 6.0 0.6 - - - +
89A TYR* 3.9 19.5 + - - +
15B VAL* 5.2 4.1 - - - +
42B LEU* 3.3 29.8 + - - +
43B HIS* 3.2 35.3 + - + +
44B MET 4.4 3.6 - - - +
45B LEU* 1.3 81.7 - - - +
62B GLU* 3.2 24.4 + - - +
63B GLU 5.4 1.5 + - - -
64B LEU* 3.8 20.8 - - + +
66B ILE* 5.1 1.6 - - - -
183B ARG* 5.6 2.6 + - - -
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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