Contacts of the helix formed by residues 22 - 41 (chain J) 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 SER 22 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J TYR 3.7 1.0 + - - -
21J GLY* 1.3 76.0 - - - -
23J GLY* 1.3 67.7 + - - +
24J HIS 3.3 2.9 + - - -
25J ASP* 3.4 20.1 + - - +
26J ARG* 3.8 21.5 - - - +
20K ASP* 3.8 25.8 + - - -
83K ASN* 4.1 8.5 - - - -
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Residues in contact with GLY 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J SER* 1.3 75.6 + - - +
24J HIS* 1.3 63.6 + - - -
26J ARG* 3.5 6.1 - - - +
27J GLU* 3.3 19.1 + - - +
66J ASP* 5.2 0.5 - - - +
16K GLN* 5.3 10.1 - - - -
83K ASN* 3.4 30.8 + - - +
84K LEU* 6.1 0.2 - - - +
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Residues in contact with HIS 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J SER 3.3 0.8 + - - -
23J GLY* 1.3 70.0 - - - -
25J ASP* 1.3 71.5 + - - +
26J ARG 2.8 3.4 + - - -
27J GLU* 2.9 34.2 + - + +
28J ALA* 2.9 14.8 + - - +
86K ASP* 3.7 38.0 + - + +
66O GLU* 4.5 19.1 - - - +
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Residues in contact with ASP 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J TYR 4.6 4.3 - - - +
21J GLY* 5.1 3.4 - - - -
22J SER 3.5 17.1 - - - +
24J HIS* 1.3 77.4 + - - +
26J ARG* 1.3 51.6 + - - +
28J ALA* 3.6 6.0 - - - +
29J PHE* 2.6 37.7 + - - +
120J GLN* 4.6 14.4 + - - +
63O ASP* 4.5 11.6 - - - +
65O HIS* 2.9 38.2 + - - +
80O LEU* 5.2 1.2 - - - +
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Residues in contact with ARG 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J TYR* 3.2 56.0 + - + +
21J GLY 3.1 23.4 + - - -
22J SER* 3.6 17.6 + - - +
23J GLY 3.5 10.0 + - - +
24J HIS 2.8 1.2 + - - -
25J ASP* 1.3 75.2 - - - +
27J GLU* 1.3 55.9 + - - +
28J ALA 2.7 16.1 + - - -
29J PHE* 2.9 7.2 + - + +
30J SER* 2.9 27.6 + - - +
66J ASP* 3.3 28.3 + - - +
23K TRP* 5.8 4.0 - - - -
79K ASP* 3.4 18.2 + - - +
80K LEU* 5.2 4.4 - - - +
83K ASN* 3.2 36.2 - - - +
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Residues in contact with GLU 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J GLY 3.3 10.3 + - - +
24J HIS* 2.9 30.9 + - - +
26J ARG* 1.3 76.5 - - - +
28J ALA* 1.3 56.4 + - - +
30J SER* 3.1 9.2 + - - -
31J GLN* 3.0 24.8 - - + +
62J ILE* 4.0 33.6 - - + +
66J ASP* 3.7 14.7 + - - +
83K ASN 5.4 1.4 - - - +
84K LEU* 4.5 10.8 - - + +
86K ASP 4.7 0.7 - - - +
87K ASP* 3.5 32.1 - - - +
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Residues in contact with ALA 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J HIS 2.9 13.3 + - - +
25J ASP* 3.6 5.2 - - - +
26J ARG 2.7 4.4 + - - -
27J GLU* 1.3 73.3 - - - +
29J PHE* 1.3 68.8 + - - +
30J SER 3.0 1.6 - - - -
31J GLN* 2.7 9.4 + - - +
32J ALA* 2.6 25.3 + - - +
78O SER* 3.6 33.0 - - - +
80O LEU* 4.3 6.5 - - + -
81O PHE* 4.5 7.0 - - + -
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Residues in contact with PHE 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J TRP* 3.8 28.5 - + - -
19J ALA* 3.5 29.2 - - + +
20J TYR* 4.2 19.5 - + - +
25J ASP 2.6 22.8 + - - +
26J ARG* 3.4 8.1 - - - +
28J ALA* 1.3 72.6 - - - +
30J SER* 1.3 63.3 + - - +
32J ALA* 3.5 2.6 + - - +
33J ILE* 3.1 44.0 + - + +
69J LEU* 3.9 9.9 - - + -
116J VAL* 3.7 25.4 - - + -
117J VAL* 3.8 28.7 - - + -
120J GLN* 3.9 14.4 - - + +
80O LEU* 4.1 10.5 - - + +
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Residues in contact with SER 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J ARG* 2.9 18.2 + - - -
27J GLU* 3.1 11.1 + - - -
29J PHE* 1.3 75.4 - - - +
31J GLN* 1.3 73.0 + - - +
33J ILE* 3.0 6.5 + - - +
34J TRP* 2.9 27.0 + - - -
62J ILE* 5.2 1.6 + - - +
65J ALA* 3.9 20.0 - - - +
66J ASP* 4.3 7.6 + - - +
69J LEU* 3.5 37.0 - - - -
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Residues in contact with GLN 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J GLU* 3.0 20.0 - - + +
28J ALA* 2.7 12.5 + - - +
30J SER* 1.3 81.3 + - - +
32J ALA* 1.3 63.6 + - - +
34J TRP* 3.1 5.1 + - - +
35J ARG* 3.0 42.5 + - - +
56J THR* 2.6 28.6 + - - +
57J SER* 3.5 22.8 + - - +
61J PHE* 5.2 2.2 - - - -
62J ILE* 3.6 29.3 - - + +
65J ALA* 5.0 2.2 - - - +
81O PHE* 3.7 20.1 - - + -
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Residues in contact with ALA 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J ALA 2.6 16.8 + - - +
29J PHE 3.6 4.9 - - - +
31J GLN* 1.3 72.0 - - - +
33J ILE* 1.3 63.9 + - - +
35J ARG* 3.2 6.9 + - - +
36J ALA* 3.0 23.2 + - - +
116J VAL* 3.9 15.0 - - + +
80O LEU* 3.9 34.8 - - + +
81O PHE* 4.2 9.5 - - + -
138O PHE* 4.9 7.1 - - + -
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Residues in contact with ILE 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J TRP* 5.6 0.4 - - + -
29J PHE* 3.1 44.9 + - + +
30J SER* 3.0 9.7 + - - +
32J ALA* 1.3 78.2 - - - +
34J TRP* 1.3 60.8 + - + +
36J ALA* 3.2 5.7 + - - +
37J THR* 2.9 25.5 + - - -
69J LEU* 4.0 15.3 - - + -
109J PHE* 4.2 20.0 - - + -
112J ALA* 3.4 9.4 - - + +
113J ILE* 3.9 37.9 - - + -
116J VAL* 3.7 24.5 - - + -
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Residues in contact with TRP 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J SER 2.9 21.6 + - - +
31J GLN* 3.7 6.1 - - - +
33J ILE* 1.3 71.7 - - + +
35J ARG* 1.3 67.6 + - + +
37J THR* 2.9 21.2 + - + -
38J PHE* 2.8 67.0 + + + +
48J PHE* 3.5 21.5 - + - -
56J THR* 5.7 0.9 - - - +
61J PHE* 3.7 24.7 - + + -
64J HIS* 4.1 7.0 - - - -
65J ALA* 3.5 37.3 - - + +
68J VAL* 4.3 4.8 - - + +
69J LEU* 4.4 11.3 - - + +
109J PHE* 3.4 31.4 - + - -
160J HEM 4.9 4.0 - + + -
161J CMO 3.2 28.5 - - - -
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Residues in contact with ARG 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J GLN* 3.0 47.0 + - - +
32J ALA* 3.5 8.1 - - - +
34J TRP* 1.3 76.0 - - - +
36J ALA* 1.3 59.0 + - - +
38J PHE* 4.1 5.2 - - - +
39J ALA* 2.9 31.6 + - - +
45J ARG* 5.9 1.1 - - - +
56J THR* 3.7 19.2 + - + +
57J SER* 3.7 11.7 + - - -
81O PHE* 3.7 23.4 - - - -
84O ASP* 3.0 17.8 + - - -
86O HIS* 3.8 41.2 - - + +
88O ASP* 2.8 42.6 + - - -
137O PHE 5.4 0.4 - - - -
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Residues in contact with ALA 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ALA 3.0 13.6 + - - +
33J ILE* 3.4 9.6 - - - +
35J ARG* 1.3 78.6 - - - +
37J THR* 1.3 63.1 + - - +
39J ALA* 3.7 2.1 - - - +
40J GLN* 3.3 24.4 + - - +
112J ALA* 3.8 19.7 - - + -
115J HIS* 5.9 1.8 - - + -
116J VAL* 4.7 6.5 - - + -
137O PHE* 4.2 28.2 - - + +
138O PHE* 4.8 9.0 - - + -
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Residues in contact with THR 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J ILE 2.9 9.0 + - - -
34J TRP* 2.9 31.2 + - + -
36J ALA* 1.3 76.4 - - - +
38J PHE* 1.3 66.4 + - + +
40J GLN* 2.9 26.4 + - - +
41J VAL* 3.1 22.3 + - + +
44J SER* 4.7 1.3 - - - +
105J TYR* 5.4 1.1 - - + +
108J ALA* 4.8 0.7 - - + -
109J PHE* 3.4 34.7 - - + +
112J ALA* 3.2 21.5 - - - +
160J HEM 5.5 5.2 - - + -
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Residues in contact with PHE 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J TRP* 2.8 47.6 + + + +
35J ARG* 4.2 3.4 - - - +
37J THR* 1.3 78.2 - - + +
39J ALA* 1.3 61.9 + - - +
41J VAL 4.4 2.9 - - - -
42J PRO* 3.0 27.5 - - - +
44J SER* 3.4 22.2 - - - -
45J ARG* 3.7 52.8 + - + +
48J PHE* 3.6 30.7 - + + -
53J GLY 4.0 15.5 - - - -
56J THR* 5.3 4.0 - - - -
61J PHE* 3.6 27.6 - + - -
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Residues in contact with ALA 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J ARG 2.9 20.7 + - - +
36J ALA* 3.7 6.3 - - - +
37J THR 3.1 0.2 - - - -
38J PHE* 1.3 78.0 - - - +
40J GLN* 1.3 62.1 + - - +
42J PRO* 4.1 5.8 - - - +
45J ARG* 5.8 0.4 - - - +
86O HIS* 6.0 4.5 - - + -
137O PHE* 4.1 24.6 - - + +
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Residues in contact with GLN 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J ALA 3.3 15.1 + - - +
37J THR* 2.9 8.2 + - - +
39J ALA* 1.3 82.2 - - - +
41J VAL* 1.3 64.6 - - + +
42J PRO* 3.5 6.7 - - - +
108J ALA* 3.0 41.2 - - + +
111J THR* 3.7 30.7 + - - +
112J ALA* 3.9 4.9 + - - +
137O PHE* 3.8 31.1 - - + -
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Residues in contact with VAL 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J THR* 3.1 16.4 + - + +
38J PHE* 3.4 3.7 - - - +
40J GLN* 1.3 83.4 - - + +
42J PRO* 1.3 62.1 - - - +
43J GLU* 2.8 9.9 + - + +
44J SER* 2.7 47.5 + - - +
104J ASN* 4.2 24.2 - - - +
105J TYR* 4.0 20.0 - - + -
108J ALA* 4.0 24.0 - - + -
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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
------------------------------------------------------------
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