Contacts of the helix formed by residues 41 - 53 (chain F) in PDB entry 2GYR
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 41 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71E ARG* 4.2 3.5 + - - -
75E TYR* 4.1 17.5 + - - -
92E ARG* 6.0 3.1 - - - -
39F ALA 2.9 7.7 + - - -
40F ARG* 1.3 77.9 - - - +
42F PRO* 1.3 71.7 - - - +
43F HIS* 3.6 11.2 + - - +
44F ASP* 2.5 56.2 + - - +
45F LEU* 3.1 5.9 + - - +
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Residues in contact with PRO 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E VAL* 6.3 2.0 - - + -
91E ASP 5.3 6.7 - - - +
92E ARG* 5.0 22.7 - - + +
93E LEU* 3.6 16.7 - - + +
40F ARG 4.7 0.2 - - - +
41F SER* 1.3 88.7 - - - +
43F HIS* 1.3 66.7 + - + +
45F LEU* 3.1 29.0 + - + +
46F SER* 3.1 10.6 + - - -
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Residues in contact with HIS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PHE* 4.2 6.4 - + - -
30E ARG 3.2 19.0 + - - -
31E PHE* 3.9 12.5 - - + +
32E CYS 5.0 0.4 - - - -
71E ARG* 5.6 0.4 - - - -
72E PRO* 4.3 16.6 - - + +
75E TYR* 3.5 26.9 - + + -
92E ARG 3.5 8.5 + - - +
93E LEU* 2.7 33.9 - - - +
94E SER* 3.8 1.1 - - - -
95E ALA* 3.4 20.6 + - - +
41F SER* 3.6 5.3 + - - +
42F PRO* 1.3 82.2 - - - +
44F ASP* 1.3 65.2 + - - +
46F SER* 4.1 0.3 - - - -
47F LEU* 3.1 43.3 + - + +
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Residues in contact with ASP 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ARG* 2.8 41.3 + - - -
40F ARG* 3.4 9.7 - - + -
41F SER* 2.5 46.5 + - - +
43F HIS* 1.3 84.1 + - - +
45F LEU* 1.3 55.8 + - - +
46F SER 3.3 0.2 - - - -
47F LEU* 3.5 5.8 - - - +
48F ALA* 2.7 36.9 + - - +
65F VAL 4.3 0.2 - - - +
66F SER* 3.1 30.4 - - - +
67F GLN* 3.9 0.4 - - - -
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Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU 5.1 0.2 - - - -
18E GLY 5.7 4.9 - - - +
19E LEU* 6.3 2.0 - - + -
40F ARG* 4.5 26.5 - - + +
41F SER 3.1 10.4 + - - +
42F PRO* 3.1 18.1 + - + +
44F ASP* 1.3 79.5 - - - +
46F SER* 1.3 57.0 + - - +
48F ALA* 3.2 5.9 + - + +
49F SER* 2.9 28.3 + - - -
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Residues in contact with SER 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ALA 4.4 0.2 - - - +
17E LEU* 2.7 37.1 + - - +
18E GLY 5.6 0.2 + - - -
19E LEU* 4.1 5.5 - - - +
29E PHE* 4.0 14.6 - - - -
93E LEU* 3.1 33.9 - - - +
42F PRO 3.1 3.8 + - - -
43F HIS 4.2 0.9 - - - -
45F LEU* 1.3 79.4 - - - +
47F LEU* 1.3 53.7 + - - +
49F SER* 3.2 2.0 + - - -
50F LEU* 2.7 41.3 + - - +
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E PHE* 4.0 10.5 - - + -
31E PHE* 4.0 23.3 - - + -
32E CYS 5.6 1.3 - - - +
71E ARG* 5.2 0.4 - - - +
43F HIS* 3.1 38.3 + - + +
44F ASP* 3.2 6.7 + - - +
46F SER* 1.3 77.6 - - - +
48F ALA* 1.3 62.8 + - - +
50F LEU* 3.7 1.3 - - - +
51F LEU* 3.1 38.2 + - + +
56F LEU* 3.6 26.2 - - + -
64F PRO* 4.8 7.9 - - + -
65F VAL 3.5 26.9 - - - +
66F SER* 4.0 8.3 - - - -
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ARG* 3.9 22.7 - - - +
44F ASP 2.7 20.4 + - - +
45F LEU* 3.5 7.2 - - + +
47F LEU* 1.3 74.9 - - - +
49F SER* 1.3 51.6 + - - +
51F LEU* 3.4 5.8 + - - +
52F GLY* 2.5 33.6 + - - -
66F SER* 4.0 11.4 - - - +
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Residues in contact with SER 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ALA 3.0 15.2 + - - +
17E LEU 4.1 0.4 - - - -
18E GLY* 3.1 27.6 + - - -
45F LEU 2.9 17.8 + - - -
46F SER 3.2 4.0 + - - -
48F ALA* 1.3 74.0 - - - +
50F LEU* 1.3 65.9 + - - +
52F GLY* 2.9 11.4 + - - +
53F ALA* 3.0 16.5 + - - +
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Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E VAL* 3.9 21.5 - - + -
16E ALA* 3.1 31.0 - - + +
17E LEU* 3.4 23.3 - - + -
29E PHE* 3.1 51.6 - - + -
46F SER 2.7 23.4 + - - +
47F LEU* 3.7 4.3 - - - +
49F SER* 1.3 71.2 - - - +
51F LEU* 1.3 58.2 + - - +
53F ALA* 2.8 19.2 + - - -
55F ALA* 3.0 24.2 + - + +
56F LEU* 3.9 18.4 - - + -
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PHE* 6.0 0.4 - - + -
47F LEU* 3.1 29.9 + - + +
48F ALA* 3.8 6.3 - - - +
50F LEU* 1.3 79.1 - - - +
52F GLY* 1.3 62.1 + - - +
53F ALA 3.1 0.9 + - - -
54F GLY* 3.1 13.5 + - - +
55F ALA 4.8 0.4 - - - +
56F LEU* 4.1 31.8 - - + +
58F PRO* 6.2 1.1 - - + -
59F PRO* 5.8 3.8 - - + -
63F ARG* 3.5 51.2 + - - +
64F PRO* 3.9 34.5 - - + +
66F SER* 5.2 6.3 - - - +
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Residues in contact with GLY 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F ALA 2.5 20.9 + - - -
49F SER* 2.9 9.3 + - - -
51F LEU* 1.3 75.7 - - - +
53F ALA* 1.3 55.5 + - - +
54F GLY 3.5 0.6 + - - -
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Residues in contact with ALA 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ALA* 4.9 11.2 - - + +
49F SER* 3.0 8.2 + - - +
50F LEU 2.8 8.2 + - - +
52F GLY* 1.3 76.7 - - - +
54F GLY* 1.3 66.6 + - - +
55F ALA* 2.7 12.1 + - + +
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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