Contacts of the helix formed by residues 21 - 38 (chain I) in PDB entry 3GHG
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 THR 21 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ASN* 5.3 3.4 - - + +
45G CYS* 3.2 22.3 - - - +
19I CYS 3.7 1.6 + - - -
20I PRO* 1.3 76.1 - - - +
22I THR* 1.3 65.1 + - - +
23I CYS* 3.1 9.2 - - + -
24I GLY* 2.9 35.5 + - - +
25I ILE* 3.2 11.8 + - - +
78K THR* 3.5 18.4 - - + +
15L PHE 5.4 0.8 + - - +
17L SER* 4.0 17.9 + - - +
19L CYS* 4.9 12.1 - - - +
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Residues in contact with THR 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G CYS* 3.4 7.6 - - - +
46G PRO* 2.2 56.6 + - - +
47G SER* 4.6 0.2 - - - -
48G GLY* 4.2 14.4 - - - +
51G MET* 4.0 11.1 - - + +
77H PRO 5.2 3.8 - - - +
79H GLY* 5.5 7.0 - - - +
82H LEU* 4.4 11.4 - - + -
20I PRO 4.0 0.2 + - - -
21I THR* 1.3 72.8 + - - +
23I CYS* 1.3 55.6 + - - +
25I ILE* 3.6 10.9 + - + +
26I ALA* 2.9 28.1 + - - +
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Residues in contact with CYS 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G TRP* 3.4 34.6 - - + -
42G ASN* 3.6 16.6 - - - +
44G LYS 3.4 7.2 - - - -
45G CYS* 2.0 54.1 - - - -
46G PRO* 3.8 5.6 - - - -
21I THR* 3.9 5.8 - - + -
22I THR* 1.3 74.7 + - - +
24I GLY* 1.3 58.8 + - - +
25I ILE 3.0 4.3 - - - -
26I ALA 2.9 16.6 + - - -
27I ASP* 3.0 17.0 + - - +
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Residues in contact with GLY 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I THR* 2.9 17.0 + - - +
23I CYS* 1.3 78.2 - - - +
25I ILE* 1.3 58.5 + - - +
27I ASP* 3.2 14.0 - - - +
28I PHE* 3.1 21.3 - - - +
14L ARG 4.6 0.3 - - - +
15L PHE* 3.4 31.4 - - - +
16L GLY* 5.4 1.6 - - - -
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Residues in contact with ILE 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G MET* 3.4 21.8 - - + -
55G ILE* 4.2 15.3 - - + -
79H GLY* 3.9 14.1 - - - +
82H LEU* 3.3 35.9 - - + -
83H GLN* 3.7 13.9 - - + +
86H LEU* 4.4 11.9 - - + -
20I PRO* 5.0 3.6 - - + +
21I THR 3.2 9.9 + - - +
22I THR* 3.8 10.8 - - - +
23I CYS 3.0 0.4 - - - -
24I GLY* 1.3 78.3 - - - +
26I ALA* 1.3 54.5 + - - +
28I PHE* 2.9 7.0 + - + +
29I LEU* 2.6 35.2 + - + +
15L PHE* 4.1 18.8 - - + -
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Residues in contact with ALA 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G TRP* 4.1 15.0 - - + -
46G PRO* 4.6 5.4 - - + -
51G MET* 3.5 23.8 - - + -
22I THR 2.9 20.2 + - - +
23I CYS* 2.9 4.7 + - - +
25I ILE* 1.3 76.3 - - - +
27I ASP* 1.3 56.7 + - - +
29I LEU* 3.2 5.8 + - - +
30I SER* 2.9 30.6 + - - -
72K LEU* 5.0 9.0 - - + -
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Residues in contact with ASP 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G TRP* 3.3 28.7 - - + -
23I CYS 3.0 17.7 + - - +
24I GLY* 3.2 17.7 - - - +
26I ALA* 1.3 74.6 - - - +
28I PHE* 1.3 74.6 + - - +
30I SER* 4.4 5.6 - - - +
31I THR* 2.4 49.8 + - + +
14L ARG 5.2 2.6 - - - +
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Residues in contact with PHE 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H LEU* 4.0 28.9 - - + -
87H LEU* 6.3 2.9 - - + -
90H GLU* 3.9 19.5 - - - -
24I GLY 3.1 20.2 - - - +
25I ILE* 2.9 7.0 + - + +
27I ASP* 1.3 80.3 + - - +
29I LEU* 1.3 68.1 + - - +
31I THR* 2.7 20.9 + - - -
32I TYR* 3.2 20.0 + + + +
14L ARG* 3.3 64.4 - - + +
15L PHE* 4.2 28.0 - + + -
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Residues in contact with LEU 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G MET* 4.6 13.0 - - + -
54G LEU* 4.3 32.5 - - + +
55G ILE* 4.6 8.7 - - + +
58G VAL* 3.4 36.6 - - + -
86H LEU* 5.1 11.0 - - + -
25I ILE* 2.6 20.3 + - + +
26I ALA* 3.2 11.2 - - - +
28I PHE* 1.3 73.4 - - - +
30I SER* 1.3 60.9 + - - +
31I THR 3.0 0.9 + - - -
32I TYR* 3.1 10.1 + - + -
33I GLN* 2.5 46.1 + - + +
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Residues in contact with SER 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ALA 2.9 18.1 + - - -
27I ASP* 4.3 5.2 - - - -
29I LEU* 1.3 76.6 - - - +
31I THR* 1.3 58.1 + - - +
33I GLN* 4.1 14.3 + - - +
34I THR* 2.6 28.3 + - - -
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Residues in contact with THR 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I ASP* 2.4 41.9 + - + +
28I PHE* 2.7 24.8 + - - +
30I SER* 1.3 74.6 - - - +
32I TYR* 1.3 67.8 + - - +
34I THR* 4.2 1.7 - - - -
35I LYS* 3.3 24.0 + - - +
14L ARG* 5.5 1.2 + - - -
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Residues in contact with TYR 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G VAL* 4.9 10.0 - - + +
59G ASN* 4.6 9.4 + - - -
62G PHE* 5.7 2.3 - + - -
86H LEU* 5.1 14.5 - - + +
89H GLN 4.4 13.7 + - - -
90H GLU* 4.2 29.6 - - + +
93H ILE* 4.8 10.8 - - + +
94H ARG* 3.9 22.7 - - + +
28I PHE* 3.6 19.1 - + + +
29I LEU* 3.1 18.0 + - + -
31I THR* 1.3 79.5 + - - +
33I GLN* 1.3 71.9 + - - +
34I THR 3.3 0.4 - - - -
35I LYS* 3.0 8.4 + - + -
36I VAL* 2.8 52.4 + - + +
14L ARG* 4.8 14.1 - - - +
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Residues in contact with GLN 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G VAL* 3.4 27.6 - - + -
62G PHE* 3.7 9.6 - - + -
29I LEU* 2.5 48.3 + - + +
30I SER* 4.3 10.9 + - - +
32I TYR* 1.3 76.6 - - - +
34I THR* 1.3 68.9 + - - +
37I ASP* 2.7 72.4 + - - +
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Residues in contact with THR 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I SER* 2.6 26.4 + - - -
31I THR 4.2 2.0 - - - -
32I TYR 3.3 0.4 - - - -
33I GLN* 1.3 92.6 + - - +
35I LYS* 1.3 58.7 + - - +
36I VAL 3.1 0.2 + - - -
37I ASP* 4.2 2.2 - - + -
38I LYS* 2.7 55.5 + - + +
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Residues in contact with LYS 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I THR 3.3 17.4 + - - +
32I TYR* 3.0 13.2 + - + +
34I THR* 1.3 76.0 - - - +
36I VAL* 1.3 60.0 + - + +
38I LYS 5.4 0.2 - - - -
39I ASP* 3.2 39.0 + - + +
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Residues in contact with VAL 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G PHE* 3.1 33.9 - - + -
93H ILE* 4.5 16.8 - - + -
94H ARG* 5.4 9.0 - - + -
97H VAL* 4.9 11.2 - - + -
32I TYR* 2.8 41.6 + - + +
33I GLN* 3.9 1.1 - - - +
35I LYS* 1.3 79.7 - - - +
37I ASP* 1.3 55.0 + - - +
38I LYS 3.2 0.9 - - - -
39I ASP* 2.7 4.8 + - - +
40I LEU* 2.6 46.8 + - + +
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Residues in contact with ASP 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ASP* 5.4 4.3 - - - +
62G PHE* 3.3 19.2 - - + -
65G ARG* 3.0 24.0 + - - +
33I GLN* 2.7 42.8 + - - +
34I THR* 4.1 2.2 - - - +
36I VAL* 1.3 76.0 - - - +
38I LYS* 1.3 72.1 - - + +
40I LEU* 3.1 18.3 + - - +
41I GLN* 3.6 3.8 + - - -
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Residues in contact with LYS 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I THR* 2.7 38.9 + - + +
35I LYS* 5.1 0.4 - - - -
37I ASP* 1.3 86.2 - - - +
39I ASP* 1.3 57.6 + - - -
40I LEU 3.5 0.2 - - - -
41I GLN* 3.8 36.3 - - + +
42I SER* 5.0 1.4 + - - -
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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
------------------------------------------------------------
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