Contacts of the helix formed by residues 28 - 46 (chain H) 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 ALA 28 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ARG* 4.4 26.7 - - + +
82E ASN* 2.8 44.8 - - - +
85E ASP* 4.8 13.0 - - + +
86E ASP* 4.8 0.4 - - - -
27H HIS* 1.3 74.8 - - + +
29H HIS* 1.3 68.9 + - + +
30H GLU* 5.6 0.2 - - - +
31H ARG* 2.9 22.5 + - - +
32H VAL* 3.8 3.1 + - - +
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Residues in contact with HIS 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ASP* 5.0 13.2 - - + +
86E ASP* 3.3 39.1 + - - +
28H ALA* 1.3 80.2 - - + +
30H GLU* 1.3 55.9 + - + +
31H ARG 2.7 12.3 + - - -
32H VAL* 2.9 16.3 + - + +
33H ALA* 3.1 14.6 + - + +
128L THR* 3.3 38.5 + - + +
129L HIS* 4.5 16.3 + + - -
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Residues in contact with GLU 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H PHE 3.9 7.9 - - - +
26H GLY* 4.4 5.6 - - - -
27H HIS* 3.1 36.8 + - - +
28H ALA* 3.1 0.4 + - - +
29H HIS* 1.3 77.6 + - + +
31H ARG* 1.3 58.2 + - - +
33H ALA* 3.5 8.7 - - - +
34H PHE* 3.3 18.9 + - - +
125H ARG* 4.3 6.2 + - - -
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Residues in contact with ARG 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E LYS* 2.4 45.1 - - - +
79E LEU* 5.2 7.9 - - - +
82E ASN* 2.9 35.7 - - - +
25H PHE* 2.9 60.2 - - + +
26H GLY 3.0 23.8 + - - +
27H HIS* 4.9 5.1 + - - -
28H ALA 2.9 9.7 + - - +
29H HIS 2.7 4.6 + - - -
30H GLU* 1.3 70.4 - - - +
32H VAL* 1.3 58.5 + - - +
33H ALA 2.9 1.3 - - - -
34H PHE* 2.6 26.9 + - - +
35H GLY* 2.7 12.3 + - - -
71H GLN* 3.1 20.0 + - - +
75H SER* 6.3 1.2 - - - -
78H ASP* 4.4 3.6 + - - -
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Residues in contact with VAL 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E ASN 5.3 0.9 - - - +
83E LEU* 4.8 9.0 - - + -
86E ASP* 3.8 34.8 - - + +
89E VAL* 5.4 13.2 - - + -
28H ALA 4.3 3.8 - - - +
29H HIS* 2.9 17.1 + - + +
31H ARG* 1.3 71.7 - - - +
33H ALA* 1.3 57.0 + - - +
35H GLY* 3.4 0.9 + - - +
36H LEU* 2.8 33.1 + - + +
67H GLY* 5.4 9.6 - - - +
70H SER* 4.9 1.2 + - - +
71H GLN* 3.4 27.1 - - - +
128L THR* 5.1 12.8 - - - +
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Residues in contact with ALA 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H HIS* 3.1 22.3 + - + +
30H GLU* 3.5 14.8 - - - +
31H ARG 2.9 0.4 - - - -
32H VAL* 1.3 77.7 - - - +
34H PHE* 1.3 61.9 + - - +
36H LEU* 3.6 5.4 - - - +
37H GLU* 2.9 25.8 + - - +
125H ARG* 4.2 10.3 + - - +
128L THR* 4.6 11.0 - - + -
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Residues in contact with PHE 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H TRP* 4.0 7.2 - + - -
24H ALA 3.9 23.1 - - - -
25H PHE* 4.4 9.9 - + + +
30H GLU 3.3 9.9 + - - +
31H ARG* 2.6 17.8 + - - +
33H ALA* 1.3 73.4 - - - +
35H GLY* 1.3 69.8 + - - +
37H GLU* 3.5 3.4 - - - +
38H LEU* 2.9 27.8 + - + -
74H LEU* 3.7 28.5 - - + -
118H LEU* 3.9 17.7 - - + -
121H VAL* 3.7 28.3 - - + +
122H LEU* 3.6 32.5 - - + -
125H ARG* 3.7 23.3 - - + +
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Residues in contact with GLY 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H ARG 2.7 15.0 + - - -
32H VAL* 3.7 2.2 - - - -
34H PHE* 1.3 82.2 - - - +
36H LEU* 1.3 62.2 + - - +
38H LEU* 3.0 3.3 + - - +
39H TRP* 3.0 26.1 + - - -
70H SER* 3.4 21.3 - - - -
71H GLN* 5.3 0.7 - - - -
74H LEU* 4.1 16.1 - - - +
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Residues in contact with LEU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H VAL* 2.8 24.9 + - + +
33H ALA* 3.6 4.5 - - - +
35H GLY* 1.3 73.0 - - - +
37H GLU* 1.3 64.9 + - - +
38H LEU 3.0 0.5 + - - -
39H TRP* 3.8 3.2 - - - +
40H ARG* 2.9 28.7 + - + +
61H ILE* 3.4 46.7 - - + +
62H TYR* 3.7 36.6 - - + +
66H PHE* 5.4 1.8 - - + -
70H SER* 4.0 4.8 + - - -
123L GLY 6.0 0.2 - - - +
127L GLY 4.4 2.9 - - - +
128L THR* 4.1 22.9 - - + +
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Residues in contact with GLU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ALA 2.9 18.6 + - - +
34H PHE* 3.5 4.9 - - - +
36H LEU* 1.3 77.6 - - - +
38H LEU* 1.3 64.0 + - - +
40H ARG* 3.5 22.1 + - - +
41H ASP* 3.2 34.0 + - - +
121H VAL* 4.0 20.0 - - + +
124H ASP* 4.2 15.4 - - - +
125H ARG* 3.3 31.1 + - - -
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Residues in contact with LEU 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H PHE* 2.9 31.1 + - + +
35H GLY* 3.2 8.7 - - - +
37H GLU* 1.3 79.2 - - - +
39H TRP* 1.3 69.9 + - + +
41H ASP* 3.2 3.8 + - - +
42H ILE* 3.1 27.8 + - + +
74H LEU* 4.5 15.5 - - + -
114H PHE* 3.9 28.5 - - + +
117H HIS* 3.7 13.9 - - + -
118H LEU* 3.7 36.3 - - + +
121H VAL* 4.0 16.3 - - + +
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Residues in contact with TRP 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H GLY* 3.0 24.9 + - - +
36H LEU* 4.1 2.5 - - - +
38H LEU* 1.3 79.7 - - + +
40H ARG* 1.3 57.6 + - - +
42H ILE* 3.2 33.3 + - + +
43H ILE* 2.8 39.2 + - + +
49H ILE* 5.0 0.9 - - + -
53H PHE* 3.5 34.5 - + - -
61H ILE* 4.8 2.2 - - + -
66H PHE* 3.7 31.4 - + + -
69H HIS* 4.9 1.1 - - - -
70H SER* 3.7 32.5 + - - +
73H VAL* 4.0 6.9 - - + +
74H LEU* 4.2 11.5 - - + +
114H PHE* 3.7 31.6 - + - -
160H HEM 4.6 11.4 - + + -
161H CMO 3.5 22.0 - - - -
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Residues in contact with ARG 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H LEU* 2.9 23.7 + - + +
37H GLU* 3.7 19.9 + - - +
39H TRP* 1.3 77.5 - - - +
41H ASP* 1.3 74.8 + - - +
43H ILE* 3.8 2.3 - - - +
44H ASP* 3.0 42.2 + - - +
61H ILE* 3.6 25.7 - - + +
62H TYR* 3.1 28.2 + - - -
120L HIS* 3.8 32.7 + - - +
123L GLY 3.8 2.4 + - - -
124L ASP* 2.7 40.2 + - - +
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Residues in contact with ASP 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H GLU* 3.2 20.0 + - - +
38H LEU* 3.2 9.5 + - - +
40H ARG* 1.3 92.7 + - - +
42H ILE* 1.3 60.9 + - - +
44H ASP* 4.1 6.4 - - - +
45H ASP* 3.4 15.1 + - - +
117H HIS* 3.2 29.6 + - + -
120H HIS* 3.9 22.1 + - - -
121H VAL* 5.3 6.0 - - + +
120L HIS* 5.3 5.0 - - - -
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Residues in contact with ILE 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H LEU* 3.1 24.8 + - + +
39H TRP* 3.5 39.7 - - + +
40H ARG 3.1 0.2 - - - -
41H ASP* 1.3 77.7 - - - +
43H ILE* 1.3 64.9 + - + +
45H ASP* 3.2 4.7 + - - +
46H HIS* 3.0 21.8 + - - +
49H ILE* 3.5 27.8 - - + -
113H ILE* 4.8 5.2 - - + -
114H PHE* 3.7 33.4 - - + -
117H HIS* 3.6 30.6 - - + +
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Residues in contact with ILE 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H TRP* 2.8 24.8 + - + +
40H ARG* 4.0 3.6 - - - +
42H ILE* 1.3 79.9 - - + +
44H ASP* 1.3 68.2 + - - +
46H HIS 4.3 4.9 - - - -
47H PRO* 3.1 24.9 - - + +
49H ILE* 4.8 11.4 - - + -
50H LYS* 3.6 34.1 - - + -
53H PHE* 4.7 11.4 - - + -
58H GLY 4.0 10.8 - - - +
61H ILE* 3.7 31.0 - - + -
66H PHE* 4.6 10.1 - - + -
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Residues in contact with ASP 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ARG* 3.0 29.7 + - - +
41H ASP* 4.1 6.5 - - - +
43H ILE* 1.3 83.5 - - - +
45H ASP* 1.3 61.7 + - - +
47H PRO* 4.0 6.8 - - - +
116L LYS* 5.9 8.8 - - - +
120L HIS* 3.8 27.5 + - - +
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Residues in contact with ASP 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ASP 3.4 15.7 + - - +
42H ILE 3.2 5.3 + - - +
43H ILE 3.2 0.2 - - - -
44H ASP* 1.3 82.7 - - - +
46H HIS* 1.3 93.9 + - + +
47H PRO* 3.8 4.3 - - - +
48H GLU* 4.4 0.3 - - - +
116H LYS* 3.3 18.5 + - - -
117H HIS* 3.8 15.5 - - + +
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Residues in contact with HIS 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ILE 3.0 9.9 + - - +
43H ILE* 3.4 5.1 - - - +
45H ASP* 1.3 110.2 + - + +
47H PRO* 1.3 54.7 - - - +
48H GLU* 2.7 45.1 + - - +
49H ILE* 3.0 30.2 + - + +
113H ILE* 3.4 42.7 - - + +
116H LYS* 4.4 6.1 + - - -
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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
------------------------------------------------------------
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