Contacts of the helix formed by residues 27 - 46 (chain I) in PDB entry 2GTL
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 PHE 27 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I SER* 3.1 15.2 + - - +
26I SER* 1.3 85.9 - - - +
28I THR* 1.3 68.2 + - - +
29I ASP* 3.3 6.6 + - - +
30I ARG* 3.8 4.0 + - - +
31I ARG* 4.3 6.0 + - - -
25K ASP* 3.3 24.2 - - - -
27K GLU* 3.8 23.1 - - + -
30K LYS* 3.5 35.2 - - + -
31K ILE* 3.7 27.8 - - + -
15L LEU* 4.1 15.5 - - + -
18L LYS* 3.8 26.0 - - + +
19L LEU* 5.6 0.7 - - + -
82L SER 4.9 2.2 - - - -
85L ASP* 4.1 20.2 - - + -
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Residues in contact with THR 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I SER 4.2 0.4 - - - -
27I PHE* 1.3 69.5 - - - +
29I ASP* 1.3 73.9 + - - -
30I ARG 2.7 3.5 + - - -
31I ARG* 3.0 33.8 + - - +
32I VAL* 3.1 16.8 + - - -
71I VAL* 4.0 21.3 - - + -
82L SER* 3.4 33.4 + - - +
83L MET* 4.3 11.7 - - + -
85L ASP* 4.8 3.5 + - - -
86L THR* 4.5 11.3 + - - +
89L MET* 4.5 14.2 - - + -
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Residues in contact with ASP 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I PHE* 4.4 6.5 - - - +
28I THR* 1.3 82.7 + - - +
30I ARG* 1.3 65.8 + - - +
32I VAL* 3.4 7.5 - - - +
33I ALA* 3.2 19.6 + - - +
80J ASP* 4.7 10.6 - - - +
81J GLN* 6.0 0.2 - - - +
27K GLU* 3.9 17.9 - - + +
30K LYS* 3.1 42.5 + - - +
85L ASP* 5.1 3.1 - - - +
86L THR* 5.6 3.8 - - - +
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Residues in contact with ARG 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASP* 3.4 22.3 + - - -
22I VAL* 3.0 32.1 + - - +
24I SER* 3.8 14.7 + - - -
25I SER* 4.1 12.6 - - - +
27I PHE 3.8 0.8 + - - -
28I THR 2.7 4.6 + - - -
29I ASP* 1.3 73.9 - - - +
31I ARG* 1.3 67.4 + - - +
32I VAL 2.9 1.7 + - - -
33I ALA* 3.0 16.6 + - - +
34I ILE* 3.1 27.9 + - + +
126I VAL* 3.8 21.0 + - - +
127I LEU* 5.3 1.0 - - - +
10J LEU* 3.5 41.1 + - + +
13J LYS* 5.8 3.6 - - - +
14J SER* 4.1 19.0 - - - +
26K THR* 4.3 11.6 + - - -
27K GLU* 3.6 17.2 + - - +
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Residues in contact with ARG 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I VAL 5.0 3.8 + - - +
23I TRP* 3.4 59.2 - - + +
25I SER 3.3 23.2 + - - -
26I SER* 4.0 13.3 - - - +
27I PHE 4.3 3.4 + - - -
28I THR* 3.0 34.8 + - - +
30I ARG* 1.3 78.3 - - - +
32I VAL* 1.3 66.0 + - + +
34I ILE* 3.3 8.8 + - - +
35I VAL* 2.9 29.4 + - - +
71I VAL* 4.5 14.5 - - + +
74I ALA* 4.6 3.8 - - + -
75I ASN* 3.0 23.5 + - - -
78L ASP* 4.0 10.5 + - - -
82L SER* 3.8 22.8 + - - -
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Residues in contact with VAL 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I THR* 3.5 22.9 - - - +
29I ASP* 3.4 10.5 - - - +
30I ARG 2.9 0.6 + - - -
31I ARG* 1.3 83.4 - - - +
33I ALA* 1.3 67.7 + - - +
34I ILE 3.0 0.7 + - - -
35I VAL* 3.7 3.6 - - - +
36I ARG* 2.8 38.6 + - - +
67I LYS* 4.8 13.5 - - + +
70I LEU* 4.3 22.3 - - + +
71I VAL* 3.8 28.0 - - + +
89L MET* 4.6 8.7 - - + -
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Residues in contact with ALA 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I ASP 3.2 7.9 + - - +
30I ARG* 3.0 9.2 + - - +
32I VAL* 1.3 82.7 - - - +
34I ILE* 1.3 57.7 + - - +
36I ARG* 3.6 10.4 - - - +
37I ALA* 2.8 30.9 + - - +
6J VAL* 4.6 18.5 - - + +
7J LEU* 5.0 1.7 - - + +
10J LEU* 4.3 17.5 - - + -
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Residues in contact with ILE 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I TRP* 6.5 0.7 - - + -
22I VAL* 4.1 28.3 - - + +
30I ARG* 3.1 31.3 + - + +
31I ARG* 3.6 8.5 - - - +
32I VAL 3.0 1.0 + - - -
33I ALA* 1.3 73.1 - - - +
35I VAL* 1.3 70.8 + - + +
37I ALA* 3.0 8.1 + - - +
38I VAL* 2.8 34.4 + - + +
119I PHE* 5.7 2.2 - - + -
122I VAL* 4.6 7.6 - - + -
123I LEU* 4.4 17.9 - - + -
126I VAL* 3.9 22.0 - - + -
7J LEU* 5.1 2.2 - - - -
10J LEU* 3.9 15.5 - - + -
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Residues in contact with VAL 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I TRP* 6.2 2.5 - - + -
23I TRP* 5.2 1.8 - - + -
31I ARG* 2.9 21.7 + - - +
32I VAL 3.9 1.8 - - - +
34I ILE* 1.3 76.5 - - + +
36I ARG* 1.3 65.4 + - - +
38I VAL* 3.1 13.3 - - + +
39I PHE* 3.0 41.8 + - + -
70I LEU* 3.7 24.9 - - + +
73I VAL* 4.3 7.6 - - + -
74I ALA* 3.3 34.8 - - + -
77I LEU* 6.3 0.4 - - + -
119I PHE* 5.6 11.4 - - + -
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Residues in contact with ARG 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I VAL* 2.8 25.6 + - - +
33I ALA* 3.6 9.2 - - - +
35I VAL* 1.3 72.4 - - - +
37I ALA* 1.3 54.7 + - - +
38I VAL 2.7 5.3 + - - -
39I PHE* 2.7 27.6 + - + +
40I ASP* 2.9 31.3 + - - +
61I PRO* 3.4 33.3 + - - +
62I GLU* 3.5 25.1 + - - -
66I PHE* 3.7 22.6 - - + -
67I LYS* 4.0 14.1 - - - +
70I LEU* 4.1 25.7 - - + +
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Residues in contact with ALA 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ALA 2.8 22.2 + - - +
34I ILE 3.4 4.7 - - - +
36I ARG* 1.3 73.2 - - - +
38I VAL* 1.3 60.7 - - - +
40I ASP* 3.8 12.8 + - - +
41I ASP* 3.5 14.4 + - - +
122I VAL* 3.8 15.4 - - + +
6J VAL* 6.2 2.7 - - + -
7J LEU* 3.8 28.7 - - + -
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Residues in contact with VAL 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I ILE* 2.8 22.7 + - + +
35I VAL* 3.1 13.2 - - + +
36I ARG 2.7 4.8 + - - -
37I ALA* 1.3 71.5 - - - +
39I PHE* 1.3 68.3 + - + +
41I ASP* 3.0 15.4 + - - +
42I LEU 3.2 7.6 + - - -
115I ILE* 4.0 10.1 - - + -
118I ALA* 3.5 23.5 - - + +
119I PHE* 3.7 49.1 - - + +
122I VAL* 3.7 24.2 - - + -
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Residues in contact with PHE 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I VAL* 3.0 38.7 + - + -
36I ARG* 2.7 12.7 + - + +
38I VAL* 1.3 69.2 - - + +
40I ASP* 1.3 57.5 + - - +
41I ASP 2.9 2.0 - - - -
42I LEU* 2.6 45.3 + - + +
43I PHE* 2.7 41.6 + + + -
53I PHE* 4.1 17.7 - + - -
66I PHE* 5.7 3.8 - + + -
69I HIS* 4.8 2.9 - + - -
70I LEU* 3.5 20.6 - - + -
73I VAL* 4.0 17.9 - - + -
115I ILE* 3.8 24.5 - - + -
160I HEM 5.3 1.6 - + - -
161I CMO 3.4 24.0 - - - -
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Residues in contact with ASP 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I ARG* 2.9 42.1 + - - +
37I ALA* 3.9 10.7 - - - +
39I PHE* 1.3 77.2 - - - +
41I ASP* 1.3 56.3 + - - +
43I PHE* 4.0 12.9 - - - +
44I LYS* 3.0 28.9 + - - +
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Residues in contact with ASP 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ALA 3.5 9.7 + - - +
38I VAL 3.0 10.9 + - - +
39I PHE 2.9 0.8 - - - -
40I ASP* 1.3 76.7 - - - +
42I LEU* 1.3 64.4 + - - +
44I LYS* 3.9 6.5 - - - +
45I HIS* 3.1 29.7 + - - +
114I GLY 4.9 0.5 - - - +
118I ALA* 3.5 20.3 + - + +
121I ARG* 2.7 46.9 + - - +
122I VAL* 4.6 6.1 - - + +
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Residues in contact with LEU 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I VAL 3.2 6.2 + - - +
39I PHE* 2.6 47.0 + - + +
41I ASP* 1.3 75.6 + - - +
43I PHE* 1.3 54.6 + - + +
45I HIS* 3.3 0.6 + - - -
46I TYR* 2.7 52.3 + - + +
49I SER* 3.9 11.4 - - - +
111I TYR* 3.9 20.6 - - - +
114I GLY 3.9 5.8 - - - -
115I ILE* 3.9 29.8 - - + +
118I ALA* 4.6 2.4 - - + +
160I HEM 4.1 22.9 - - + -
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Residues in contact with PHE 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I PHE* 2.7 41.4 + + + +
40I ASP* 4.0 13.0 - - - +
42I LEU* 1.3 84.8 - - + +
44I LYS* 1.3 63.8 + - - +
45I HIS 3.1 2.5 - - - -
46I TYR 4.2 3.6 - - - -
47I PRO* 3.1 27.5 - - - +
49I SER* 3.4 22.7 - - - -
50I LYS* 3.8 48.7 - - + +
53I PHE* 3.9 29.8 - + - -
58I ILE* 5.1 11.4 - - + -
66I PHE* 5.3 7.9 - + - -
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Residues in contact with LYS 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I ASP 3.0 19.4 + - - +
41I ASP* 4.2 3.4 - - - +
42I LEU 3.3 0.2 - - - -
43I PHE* 1.3 76.3 - - - +
45I HIS* 1.3 79.9 + - + +
47I PRO* 4.5 3.4 - - - +
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Residues in contact with HIS 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ASP* 3.1 26.0 + - - +
42I LEU 3.3 1.2 + - - -
44I LYS* 1.3 101.6 - - + +
46I TYR* 1.3 82.7 - + + +
47I PRO* 3.3 11.2 - - - +
117I GLU* 5.1 3.8 - - - -
121I ARG* 3.3 34.9 + - - +
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Residues in contact with TYR 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I LEU* 2.7 32.4 + - + +
43I PHE* 4.2 0.2 - - - -
45I HIS* 1.3 94.5 - + + +
47I PRO* 1.3 55.6 - - - +
48I THR* 2.9 13.5 + - - +
49I SER* 2.7 29.5 + - - -
110I GLU* 3.5 45.3 - - + -
111I TYR* 4.1 22.0 - + + -
113I ARG* 3.6 16.6 + - - -
114I GLY* 3.8 15.6 - - - -
117I GLU* 3.0 33.4 + - - -
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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