Contacts of the helix formed by residues 48 - 66 (chain A) in PDB entry 4TLG
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 ASP 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ARG 2.9 16.1 + - - +
46A ASN* 3.1 3.9 + - + +
47A PHE* 1.3 73.3 - - - +
49A LEU* 1.3 60.6 + - - +
50A GLN* 3.2 10.9 + - - +
51A LYS* 3.0 56.0 + - + +
52A SER* 2.8 36.4 + - - -
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Residues in contact with LEU 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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15A ALA* 3.3 36.3 - - + +
18A ARG* 4.1 17.5 - - + -
19A PHE* 3.8 30.0 - - + +
22A ASN* 4.6 12.2 + - - +
42A LEU* 4.4 6.1 - - + -
47A PHE 3.0 12.5 + - - +
48A ASP* 1.3 71.5 + - - +
50A GLN* 1.3 61.9 + - - +
52A SER* 4.0 4.5 - - - -
53A GLU* 3.1 26.7 + - - +
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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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48A ASP* 3.2 7.9 + - - +
49A LEU* 1.3 78.1 - - - +
51A LYS* 1.3 63.3 + - + +
53A GLU* 3.3 20.8 + - - +
54A ASP* 2.9 35.2 + - + +
280B HIS* 5.8 2.7 - - - +
281B THR* 3.3 23.5 + - - +
282B ARG* 3.1 43.0 - - - +
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Residues in contact with LYS 51 (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 ARG* 3.9 30.9 + - + +
48A ASP* 3.0 33.9 + - + +
50A GLN* 1.3 78.9 - - + +
52A SER* 1.3 57.3 + - - +
54A ASP* 3.3 7.2 + - - +
55A MET* 2.8 31.0 + - - +
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Residues in contact with SER 52 (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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19A PHE* 3.7 20.9 - - - -
41A TRP* 3.4 24.6 + - - +
42A LEU* 3.5 23.1 + - - +
45A ARG* 3.5 14.0 - - - +
48A ASP 2.8 24.5 + - - -
49A LEU 4.0 1.1 - - - -
51A LYS* 1.3 76.2 - - - +
53A GLU* 1.3 58.0 + - - +
55A MET* 3.4 2.8 + - - +
56A LEU* 3.0 29.3 + - - +
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Residues in contact with GLU 53 (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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19A PHE* 3.6 13.3 - - + -
22A ASN* 3.7 32.3 + - - +
23A LEU* 4.2 9.6 - - + -
49A LEU 3.1 19.1 + - - +
50A GLN* 3.6 20.9 - - - +
52A SER* 1.3 74.5 - - - +
54A ASP* 1.3 59.0 + - - +
56A LEU* 3.8 2.5 - - - +
57A ARG* 2.8 76.7 + - + +
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Residues in contact with ASP 54 (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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50A GLN* 2.9 26.2 + - + +
51A LYS* 3.5 8.3 - - - +
53A GLU* 1.3 77.6 - - - +
55A MET* 1.3 61.9 + - - +
57A ARG* 4.1 4.8 - - - +
58A ARG* 2.9 49.6 + - - +
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Residues in contact with MET 55 (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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41A TRP* 3.7 18.7 - - + +
44A ALA* 3.8 23.8 - - + -
45A ARG* 3.6 48.7 - - - +
51A LYS 2.8 17.2 + - - +
52A SER* 3.7 4.9 - - - +
54A ASP* 1.3 78.2 - - - +
56A LEU* 1.3 62.6 + - - +
58A ARG* 3.4 7.9 + - - +
59A HIS* 3.1 21.5 + - - +
179A GLU 3.3 26.7 - - - +
180A ALA* 3.8 16.8 - - + +
183A PRO* 4.1 10.8 - - + -
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Residues in contact with LEU 56 (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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19A PHE* 4.1 8.7 - - + -
23A LEU* 3.6 39.3 - - + -
26A LEU* 5.0 0.7 - - + -
30A LEU* 4.2 7.2 - - + -
37A PHE* 3.7 28.3 - - + -
38A LEU* 4.5 2.2 - - + -
41A TRP* 3.6 41.9 - - + -
52A SER 3.0 17.0 + - - +
53A GLU* 4.0 3.1 - - - +
55A MET* 1.3 78.0 - - - +
57A ARG* 1.3 58.9 + - - +
59A HIS* 3.1 6.0 + - + +
60A MET* 2.9 41.6 + - + +
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Residues in contact with ARG 57 (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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22A ASN 3.1 21.2 + - - -
23A LEU* 4.2 7.0 - - + +
25A ASP* 2.8 42.6 + - - -
26A LEU* 3.5 25.1 - - + +
53A GLU* 2.8 50.8 + - + +
54A ASP* 4.1 4.9 - - - +
56A LEU* 1.3 68.6 - - - +
58A ARG* 1.3 64.9 + - - +
60A MET* 3.2 9.2 + - - +
61A GLU* 2.9 23.6 + - - +
515A EDO 5.2 0.5 + - - -
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Residues in contact with ARG 58 (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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54A ASP* 2.9 43.4 + - - +
55A MET* 3.6 7.2 - - - +
57A ARG* 1.3 75.3 - - - +
59A HIS* 1.3 63.8 + - - +
61A GLU* 3.3 7.6 + - - +
62A PHE* 3.0 22.0 + - - +
181A ASN* 5.0 0.4 - - - -
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Residues in contact with HIS 59 (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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31A PRO* 5.0 2.2 - - + -
37A PHE* 5.1 0.2 - + - -
41A TRP* 3.6 29.4 - + + -
55A MET 3.1 11.2 + - - +
56A LEU* 3.1 9.6 + - + +
58A ARG* 1.3 76.7 - - - +
60A MET* 1.3 67.0 + - - +
62A PHE* 3.0 3.5 + - - +
63A ARG* 2.8 74.0 + - + +
68A LEU* 4.5 4.7 - - + -
180A ALA 4.5 2.0 + - - +
181A ASN* 2.9 48.5 + - + +
182A TYR* 4.5 7.6 - - - -
502A EDO 3.2 18.2 - - - -
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Residues in contact with MET 60 (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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26A LEU* 4.0 19.3 - - + -
29A ILE* 3.4 43.3 - - + +
30A LEU* 3.8 19.7 - - + -
31A PRO* 4.0 6.3 - - - -
56A LEU* 2.9 23.7 + - + +
57A ARG* 3.7 6.7 - - - +
59A HIS* 1.3 82.1 - - - +
61A GLU* 1.3 61.4 + - - +
63A ARG* 3.3 23.7 + - - +
64A LYS 3.2 10.0 + - - -
515A EDO 2.8 59.5 + - - +
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Residues in contact with GLU 61 (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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57A ARG 2.9 12.9 + - - +
58A ARG* 3.6 10.5 - - - +
59A HIS 3.2 0.2 - - - -
60A MET* 1.3 78.1 - - - +
62A PHE* 1.3 57.2 + - - +
64A LYS* 3.2 31.1 + - - +
65A GLN* 2.8 64.3 + - - +
515A EDO 4.4 7.4 + - - -
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Residues in contact with PHE 62 (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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58A ARG 3.0 12.8 + - - +
59A HIS* 3.0 8.7 + - - +
61A GLU* 1.3 76.6 - - - +
63A ARG* 1.3 61.8 + - - +
65A GLN* 4.0 16.3 + - - +
66A GLN* 2.9 51.4 + - + +
68A LEU* 4.0 18.2 - - + -
125A ILE* 3.7 33.7 - - + -
177A ILE* 4.2 19.1 - - + -
181A ASN* 3.3 37.5 - - + +
182A TYR* 5.5 0.7 - + - -
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Residues in contact with ARG 63 (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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29A ILE 5.5 1.0 + - - -
31A PRO* 3.8 24.3 - - - +
59A HIS* 2.8 56.6 + - + +
60A MET* 3.5 31.2 - - - +
61A GLU 3.3 0.4 - - - -
62A PHE* 1.3 72.7 - - - +
64A LYS* 1.3 57.7 + - - +
67A ASP* 3.0 9.5 + - - -
68A LEU* 3.0 48.8 + - + +
69A ASP* 2.8 32.3 + - - +
129A GLU* 2.8 43.4 + - - -
502A EDO 4.0 4.2 - - - -
515A EDO 4.1 4.7 - - - +
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Residues in contact with LYS 64 (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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60A MET 3.2 9.4 + - - +
61A GLU* 3.2 33.5 + - - +
63A ARG* 1.3 77.3 - - - +
65A GLN* 1.3 68.2 + - + +
66A GLN 3.2 0.7 + - - -
67A ASP* 3.2 11.9 + - - +
515A EDO 3.9 18.5 + - - +
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Residues in contact with GLN 65 (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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61A GLU* 2.8 54.4 + - - +
62A PHE* 3.9 19.3 + - - +
64A LYS* 1.3 75.9 - - + +
66A GLN* 1.3 72.9 + - + +
67A ASP 3.7 0.3 + - - -
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Residues in contact with GLN 66 (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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62A PHE* 2.9 53.6 + - + +
65A GLN* 1.3 88.0 + - - +
67A ASP* 1.3 68.4 + - - +
68A LEU* 3.3 20.1 + - + +
122A ARG* 2.8 48.3 + - - +
125A ILE* 5.1 5.3 - - + +
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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