Contacts of the helix formed by residues 38 - 50 (chain A) in PDB entry 3GXL
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 GLU 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.7 35.7 - - + -
17A GLY* 4.1 7.8 + - - -
33A ILE 4.7 0.2 - - - +
34A PHE* 3.4 22.4 - - + +
35A SER* 2.9 43.2 + - - +
37A ARG* 1.3 94.8 + - + +
39A GLU* 1.3 61.8 + - - +
40A ARG 3.3 3.1 - - - -
41A SER* 3.1 9.9 + - - +
42A TRP* 3.1 21.4 + - - +
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER 3.8 1.0 + - - -
36A SER* 3.3 17.8 + - - +
37A ARG 3.3 2.0 + - - -
38A GLU* 1.3 77.9 - - - +
40A ARG* 1.3 59.4 + - + +
42A TRP* 3.2 14.5 + - + -
43A PHE* 2.7 38.9 + - + +
76A LEU* 3.6 23.9 - - + +
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG 5.1 1.5 + - - +
38A GLU 3.3 0.8 + - - -
39A GLU* 1.3 78.9 - - + +
41A SER* 1.3 57.8 + - - +
43A PHE* 3.9 5.5 - - - +
44A ARG* 3.0 30.8 + - - +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ARG* 5.1 3.1 + - - -
16A PHE* 3.5 31.7 - - - -
34A PHE* 4.2 16.1 - - - -
38A GLU* 3.1 11.8 + - - +
40A ARG* 1.3 76.0 - - - +
42A TRP* 1.3 67.5 + - - +
44A ARG* 4.0 3.9 - - - +
45A GLU* 3.1 25.8 + - - +
153A GLY* 5.2 2.9 - - - +
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Residues in contact with TRP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PHE* 3.7 30.9 - + + -
38A GLU 3.1 12.0 + - - +
39A GLU* 3.5 22.7 - - + +
41A SER* 1.3 78.6 - - - +
43A PHE* 1.3 91.4 + + + +
45A GLU* 3.9 1.7 - - - +
46A ALA* 2.9 26.1 + - + +
65A ALA* 4.1 17.9 - - + -
66A ASP* 3.7 8.7 - - - -
67A ASN* 3.6 25.6 - - - -
76A LEU* 3.6 33.4 - - + -
77A TRP 2.9 24.1 + - - +
78A LEU* 3.6 25.4 - - + +
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Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLU* 2.7 26.0 + - + +
40A ARG* 3.9 4.9 - - - +
42A TRP* 1.3 96.4 - + + +
44A ARG* 1.3 63.1 + - + +
46A ALA* 3.1 8.7 + - + +
47A GLU* 2.8 55.3 + - + +
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG 3.0 18.8 + - - +
41A SER* 4.0 5.4 - - - +
43A PHE* 1.3 81.9 - - + +
45A GLU* 1.3 63.0 + - - +
47A GLU* 2.8 38.0 + - - +
48A ILE* 3.0 37.3 + - + +
153A GLY 3.5 21.5 - - - +
155A ALA 3.0 26.7 + - - -
156A VAL* 3.9 3.0 - - - +
157A ARG* 4.1 0.2 - - - +
166A ASP* 2.8 51.8 + - - +
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Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LYS* 2.9 36.6 + - - -
34A PHE* 4.0 5.7 - - - -
41A SER 3.1 17.2 + - - +
42A TRP 4.0 2.5 - - - +
44A ARG* 1.3 73.6 - - - +
46A ALA* 1.3 67.2 + - - +
48A ILE* 3.2 3.5 + - - +
49A TYR* 3.0 52.0 + - + -
78A LEU* 3.7 16.8 - - + +
151A ASP* 3.4 15.6 - - - -
152A LEU 4.4 0.2 - - - -
153A GLY* 3.7 28.7 - - - +
999A QIG 3.8 3.3 - - - +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TRP* 2.9 18.6 + - + +
43A PHE* 3.4 14.6 - - + +
45A GLU* 1.3 76.9 - - - +
47A GLU* 1.3 62.7 + - - +
49A TYR* 3.4 1.4 + - - +
50A GLN* 3.0 38.0 + - - +
62A PHE* 4.5 5.8 - - - -
65A ALA* 4.0 17.0 - - + -
78A LEU* 3.9 21.2 - - + +
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 2.8 40.0 + - + +
44A ARG* 2.8 36.1 + - - +
46A ALA* 1.3 77.5 - - - +
48A ILE* 1.3 62.7 + - - +
50A GLN* 3.3 14.7 + - - +
51A THR 3.5 6.9 + - - -
157A ARG* 3.4 36.3 + - - +
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Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ARG* 3.0 47.0 + - + +
45A GLU 3.7 5.8 - - - +
47A GLU* 1.3 76.2 - - - +
49A TYR* 1.3 61.6 + - - +
51A THR* 2.7 27.3 + - - +
54A LEU* 3.4 5.9 - - + +
129A ILE* 4.7 11.2 - - + -
152A LEU* 3.5 48.9 - - + +
155A ALA* 4.1 15.5 - - + +
157A ARG* 3.7 28.5 - - + +
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Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.0 54.2 + - + +
46A ALA 3.8 3.6 - - - +
48A ILE* 1.3 77.4 - - - +
50A GLN* 1.3 59.7 + - - +
51A THR 3.2 3.3 + - - +
54A LEU* 3.6 20.7 - - + +
55A ARG* 6.0 1.7 - - - +
59A ILE* 4.6 2.2 - - + -
60A LEU* 3.6 35.6 - - + +
62A PHE* 3.5 52.5 - + + +
149A ILE 4.3 0.2 + - - -
150A ALA* 3.6 10.9 - - - -
151A ASP 3.5 20.8 + - - -
152A LEU* 3.6 29.2 - - + +
999A QIG 3.6 13.6 - - + +
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 3.0 34.8 + - - +
47A GLU* 3.3 8.3 + - - +
48A ILE 3.1 1.0 - - - -
49A TYR* 1.3 76.9 - - - +
51A THR* 1.3 66.2 + - - +
52A VAL* 3.4 4.9 + - - +
62A PHE* 4.1 17.2 - - + -
65A ALA* 4.1 16.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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