Contacts of the helix formed by residues 21 - 37 (chain G) in PDB entry 3ECS
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 ALA 21 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ASP 3.9 2.0 + - - -
20G MSE 1.3 79.8 - - - +
22G SER* 1.3 67.1 + - - +
23G ALA* 4.3 5.2 - - + +
24G VAL* 3.1 20.4 + - + +
25G ALA* 2.9 19.7 + - - +
108G ARG* 4.0 21.0 - - - +
132G ARG* 4.4 7.4 - - - +
231G GLU* 4.3 12.6 - - - +
233G PHE* 4.4 6.5 - - + -
234G LYS* 5.5 2.9 - - - -
507G SO4 4.6 6.7 - - - +
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Residues in contact with SER 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G PHE* 3.4 7.3 - - - -
14G MSE 3.8 17.5 - - - -
20G MSE 3.8 2.0 + - - -
21G ALA* 1.3 71.6 - - - +
23G ALA* 1.3 73.4 + - - +
25G ALA* 2.9 4.2 + - - +
26G ALA* 2.8 20.5 + - - +
60G ASP* 3.8 30.1 - - - -
62G SER* 3.3 22.6 + - - -
64G ALA* 4.4 3.1 - - - +
65G VAL* 4.2 2.6 - - - +
132G ARG* 5.1 7.3 - - - +
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Residues in contact with ALA 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ALA* 3.2 1.7 - - + -
22G SER* 1.3 82.2 + - - +
24G VAL* 1.3 62.4 + - - +
26G ALA* 3.0 17.7 + - - +
27G ILE* 3.2 19.4 + - - +
64G ALA* 3.5 35.0 - - + +
65G VAL* 4.4 1.1 - - - +
68G GLY* 5.0 3.7 - - - -
104G ILE* 5.8 0.2 - - - -
233G PHE* 3.4 34.1 - - + -
234G LYS* 5.8 0.2 - - - -
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Residues in contact with VAL 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G MSE 3.8 29.6 - - + -
21G ALA* 3.1 15.0 + - + +
23G ALA* 1.3 76.6 - - - +
25G ALA* 1.3 62.4 + - - +
27G ILE* 3.4 9.5 + - - +
28G ARG* 3.2 20.9 + - - +
101G LEU* 4.1 21.1 - - + -
104G ILE* 3.6 26.2 - - + +
105G SER* 6.0 4.0 - - - -
108G ARG* 5.8 2.5 - - - +
233G PHE* 4.0 22.0 - - + -
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Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G PHE* 3.3 13.0 - - + -
13G GLN* 3.8 15.7 - - + +
14G MSE 3.5 26.5 - - + -
20G MSE 3.9 13.9 - - - +
21G ALA 2.9 9.6 + - - +
22G SER 2.9 8.3 + - - +
24G VAL* 1.3 76.6 - - - +
26G ALA* 1.3 53.4 + - - +
28G ARG* 3.5 3.8 + - - +
29G THR* 2.7 36.9 + - - +
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Residues in contact with ALA 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G PHE* 3.1 20.6 - - + -
22G SER 2.8 10.9 + - - +
23G ALA* 3.0 11.8 + - - +
25G ALA* 1.3 76.2 - - - +
27G ILE* 1.3 65.9 + - + +
29G THR* 3.5 5.2 + - - -
30G LEU* 3.1 29.7 + - + +
57G CYS* 4.7 7.5 - - + -
65G VAL* 4.2 26.0 - - + +
69G GLY* 6.0 1.3 - - - +
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Residues in contact with ILE 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ALA 3.2 15.4 + - - +
24G VAL* 3.4 10.5 - - - +
26G ALA* 1.3 74.5 - - + +
28G ARG* 1.3 65.1 + - - +
30G LEU* 3.3 11.2 - - - +
31G LEU* 2.8 30.4 + - + +
68G GLY* 4.6 13.2 - - - +
69G GLY* 4.9 2.7 - - - +
72G PHE* 4.3 23.7 - - + -
100G PHE* 3.5 30.7 - - + -
101G LEU* 3.6 24.2 - - + -
104G ILE* 3.3 30.1 - - + -
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Residues in contact with ARG 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G TYR* 4.0 1.3 - - + -
13G GLN* 2.9 31.6 - - - +
20G MSE 2.9 38.1 - - - +
24G VAL* 3.2 11.0 + - - +
25G ALA 3.7 5.6 - - - +
26G ALA 3.2 0.4 - - - -
27G ILE* 1.3 79.2 - - - +
29G THR* 1.3 65.8 + - - +
30G LEU 3.0 1.6 - - - -
31G LEU* 3.0 12.8 + - - +
32G GLU* 2.9 26.3 + - - +
101G LEU* 3.1 48.0 + - + +
105G SER* 5.5 5.5 - - - -
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Residues in contact with THR 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MSE 4.1 4.3 - - - +
6G LEU* 3.8 18.8 + - - +
9G TYR* 3.2 29.2 - - + -
10G PHE* 3.4 37.5 - - + -
13G GLN* 4.5 1.3 - - + -
25G ALA 2.7 28.5 - - - +
26G ALA 3.5 5.6 + - - +
28G ARG* 1.3 76.0 - - - +
30G LEU* 1.3 59.5 + - - +
32G GLU* 3.6 2.3 + - - +
33G PHE* 2.8 27.4 + - - +
57G CYS* 3.8 11.1 - - - -
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Residues in contact with LEU 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LEU* 5.3 1.1 - - + -
26G ALA* 3.1 21.1 + - + +
27G ILE* 3.3 14.4 - - + +
28G ARG 3.0 0.4 - - - -
29G THR* 1.3 80.6 - - - +
31G LEU* 1.3 64.2 + - - +
33G PHE* 3.6 4.6 - - + +
34G LEU* 3.1 23.7 + - - +
50G THR* 4.2 14.7 + - - +
53G ILE* 3.3 35.2 - - + +
54G GLU* 4.1 30.5 - - + +
57G CYS* 5.3 4.9 - - - -
69G GLY* 4.5 7.0 - - - -
72G PHE* 3.9 31.6 - - + -
73G LEU* 6.1 0.7 - - + -
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Residues in contact with LEU 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ILE* 2.8 13.3 + - + +
28G ARG* 3.0 8.5 + - - +
30G LEU* 1.3 75.6 - - - +
32G GLU* 1.3 60.6 + - - +
34G LEU* 3.3 7.6 + - + +
35G LYS* 2.7 51.5 + - - +
72G PHE* 4.3 12.3 - - + -
94G ILE* 4.0 26.7 - - + +
97G GLY* 3.9 36.8 - - - +
98G GLU* 4.0 11.7 - - + +
101G LEU* 3.7 30.1 - - + -
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Residues in contact with GLU 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MSE 4.0 7.9 - - - -
9G TYR* 3.1 40.2 + - + +
28G ARG* 2.9 27.2 + - - +
29G THR 3.8 7.2 - - - +
31G LEU* 1.3 82.8 - - - +
33G PHE* 1.3 58.9 + - - +
35G LYS* 2.9 40.0 + - + +
36G ARG* 2.6 41.1 + - + +
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Residues in contact with PHE 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MSE 3.6 38.9 + - + -
2G ASP* 5.3 0.2 - - - -
3G ASP 5.9 0.2 - - - -
6G LEU* 3.6 33.7 - - + -
29G THR 2.8 18.3 + - - +
30G LEU* 3.6 11.7 - - + +
31G LEU 3.3 0.2 - - - -
32G GLU* 1.3 74.6 - - - +
34G LEU* 1.3 56.3 + - - +
36G ARG* 3.6 1.2 - - - +
37G ASP* 2.8 59.0 + - - +
46G ARG* 5.6 2.5 - - - -
49G LEU* 3.5 45.5 - - + -
50G THR* 4.0 15.3 - - - -
53G ILE* 3.7 22.2 - - + -
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Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU 3.1 14.1 + - - +
31G LEU* 3.4 11.0 - - + +
33G PHE* 1.3 84.8 - - + +
35G LYS* 1.3 55.3 + - - +
37G ASP* 2.6 35.7 + - - +
46G ARG* 4.4 18.2 - - + +
50G THR* 5.4 7.9 - - - +
72G PHE* 5.3 1.3 - - + -
76G ILE* 4.3 23.1 - - + -
91G LYS* 3.9 20.6 - - + -
93G MSE 4.5 9.0 - - + +
94G ILE* 3.5 46.0 - - + +
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Residues in contact with LYS 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G LEU* 2.7 43.6 + - - +
32G GLU* 2.9 31.7 + - + +
34G LEU* 1.3 74.3 - - - +
36G ARG* 1.3 56.4 + - - +
37G ASP 2.7 17.7 + - - +
38G LYS* 3.6 18.3 - - - +
91G LYS* 4.2 1.9 + - - -
94G ILE* 4.0 42.2 - - + -
98G GLU* 3.9 17.5 + - - +
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Residues in contact with ARG 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MSE 3.4 35.8 - - + +
2G ASP* 4.8 2.6 + - - -
5G GLU* 3.4 32.5 + - - +
32G GLU* 2.6 25.8 + - + +
35G LYS* 1.3 73.1 - - - +
37G ASP* 1.3 56.3 + - - -
38G LYS* 3.8 8.9 + - - +
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Residues in contact with ASP 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MSE 4.3 11.2 + - - +
33G PHE* 2.8 43.2 + - + +
34G LEU* 2.6 16.5 - - - +
35G LYS 2.7 1.4 + - - +
36G ARG* 1.3 78.0 - - - +
38G LYS* 1.3 65.7 + - - +
39G GLY 4.1 6.2 - - - +
46G ARG* 2.3 50.1 + - - +
49G LEU* 4.0 16.9 - - - +
91G LYS* 2.8 8.7 + - - -
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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
------------------------------------------------------------
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