Contacts of the helix formed by residues 57 - 73 (chain A) in PDB entry 1ESG
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 VAL 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLY* 1.3 73.7 - - - +
58A VAL* 1.3 72.7 + - + +
59A PRO* 3.2 3.1 - - - -
60A ILE* 2.9 25.2 + - + +
61A LYS 3.3 6.6 + - - -
112A PHE* 4.0 27.1 - - + -
113A GLU 5.1 1.3 - - - +
114A THR* 3.9 28.1 - - + +
144A PRO* 5.3 1.8 - - + -
152A LEU* 4.1 27.4 - - + -
153A THR* 4.0 13.4 + - - +
156A VAL* 4.3 14.4 - - + -
179A PHE* 4.9 2.9 - - + -
4C A 5.4 3.2 + - - +
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Residues in contact with VAL 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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57A VAL* 1.3 79.7 - - + +
59A PRO* 1.3 63.8 - - + +
61A LYS* 3.1 11.7 + - - +
62A GLU* 2.8 38.4 + - + +
114A THR* 4.1 27.4 - - + +
194A GLY 3.9 7.9 - - - +
195A SER* 3.8 26.9 - - - +
3C G 3.8 30.1 - - - +
4C A 4.0 10.3 + - - +
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Residues in contact with PRO 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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56A GLY 4.2 0.9 - - - -
57A VAL* 3.3 8.1 - - - +
58A VAL* 1.3 97.4 - - + +
60A ILE* 1.3 55.8 + - - +
62A GLU* 3.4 8.6 + - + +
63A LEU 3.0 22.3 + - - -
191A ILE* 4.0 12.3 - - + -
192A PRO 3.4 26.5 - - - +
194A GLY 4.4 10.5 - - - +
198A MET* 4.1 27.4 - - + +
203A ILE* 4.7 4.8 - - + +
206A TRP* 3.4 24.9 - - + -
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Residues in contact with ILE 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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1A MET* 4.1 22.0 - - + -
33A ILE* 4.7 3.4 - - + -
36A PRO* 4.5 15.2 - - + +
45A PHE* 4.0 13.2 - - + -
47A ILE* 5.7 0.4 - - + -
56A GLY 4.5 1.3 - - - +
57A VAL* 2.9 28.9 + - + +
59A PRO* 1.3 74.6 - - - +
61A LYS* 1.3 66.5 + - - +
63A LEU* 3.3 3.0 + - - +
64A CYS* 2.9 22.5 + - - +
112A PHE* 3.8 19.5 - - + -
148A LEU* 5.6 1.8 - - + -
152A LEU* 4.8 7.9 - - + -
179A PHE* 4.8 5.6 - - + -
191A ILE* 3.9 27.8 - - + -
206A TRP* 4.1 18.2 - - + -
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Residues in contact with LYS 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 VAL 3.3 2.4 + - - -
58A VAL* 3.1 16.8 + - - +
60A ILE* 1.3 81.0 - - - +
62A GLU* 1.3 74.3 + - - +
64A CYS* 3.1 2.4 + - - +
65A TYR* 2.9 53.7 + - + +
76A ARG* 5.7 1.8 - - - +
94A ASP* 4.8 5.9 + - - -
112A PHE* 3.5 46.1 + - + +
114A THR* 3.0 39.1 + - + -
3C G 4.5 8.9 + - - -
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Residues in contact with GLU 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 VAL* 2.8 26.5 + - + +
59A PRO* 3.5 7.9 - - + +
61A LYS* 1.3 84.6 - - - +
63A LEU* 1.3 61.7 + - - +
65A TYR* 3.5 1.6 + - - +
66A THR* 2.9 32.1 + - - +
76A ARG* 3.2 32.9 + - - +
195A SER 5.3 7.6 - - - +
200A LYS* 5.6 3.8 + - - -
203A ILE* 3.3 35.0 - - + -
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Residues in contact with LEU 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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36A PRO* 3.7 30.5 - - + -
59A PRO 3.0 13.0 + - - +
60A ILE 3.5 7.2 - - - +
62A GLU* 1.3 77.6 - - - +
64A CYS* 1.3 62.1 + - - +
66A THR* 3.2 3.9 + - - -
67A LEU* 3.0 49.8 + - + +
203A ILE* 4.3 13.9 - - + +
206A TRP* 3.2 64.4 - - + +
207A LYS* 4.5 7.0 - - + -
208A ASP* 4.1 8.1 - - - +
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Residues in contact with CYS 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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32A SER* 3.3 39.4 + - - +
33A ILE* 4.6 3.6 - - + -
36A PRO* 5.4 2.2 - - + +
60A ILE* 2.9 16.6 + - + +
61A LYS 3.5 4.5 - - - +
63A LEU* 1.3 78.2 - - - +
65A TYR* 1.3 62.8 + - - +
67A LEU* 3.4 4.8 + - - +
68A LEU* 3.2 31.4 + - - +
110A MET* 4.2 4.9 - - - -
112A PHE* 4.1 13.9 - - + -
142A LEU* 3.9 26.7 - - - -
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Residues in contact with TYR 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 LYS* 2.9 41.6 + - + +
62A GLU* 4.0 3.1 - - - +
64A CYS* 1.3 78.5 - - - +
66A THR* 1.3 62.5 + - - +
68A LEU* 3.3 7.4 + - - +
69A GLU* 3.1 31.7 + - - +
76A ARG* 3.5 39.5 - - - +
94A ASP* 2.5 44.4 + - + +
95A VAL* 3.7 21.4 - - + +
110A MET* 3.8 31.4 - - + -
111A GLU* 3.6 0.5 - - - -
112A PHE* 2.9 30.6 + - + +
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Residues in contact with THR 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 GLU* 2.9 25.1 + - - +
63A LEU* 3.5 8.3 - - + -
65A TYR* 1.3 78.0 - - - +
67A LEU* 1.3 55.5 + - - +
69A GLU* 3.4 13.1 + - - +
70A ASP* 2.9 48.7 + - - +
76A ARG* 4.8 4.5 + - - -
203A ILE* 4.5 13.2 - - + +
204A LYS* 6.3 0.7 - - - -
207A LYS* 3.6 24.7 - - - +
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Residues in contact with LEU 67 (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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32A SER* 3.8 22.2 - - - +
35A SER* 3.7 30.7 - - - +
63A LEU* 3.0 37.4 + - + +
64A CYS* 3.7 4.3 - - - +
66A THR* 1.3 74.3 - - - +
68A LEU* 1.3 60.1 + - - +
71A THR* 2.8 39.1 + - - +
72A TYR* 3.5 5.4 + - + -
207A LYS* 3.4 34.8 - - + +
208A ASP* 4.3 8.5 - - - +
209A LYS* 4.1 18.2 - - + -
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Residues in contact with LEU 68 (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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28A GLU 3.7 21.1 - - - +
29A VAL* 4.1 4.5 - - + -
32A SER* 3.6 22.4 - - - +
64A CYS* 3.2 17.1 + - - +
65A TYR* 3.3 8.9 + - - +
67A LEU* 1.3 78.0 - - - +
69A GLU* 1.3 57.8 + - - +
72A TYR* 3.1 14.4 + - + -
73A ASN 3.0 12.0 + - - -
74A TRP* 2.9 59.8 + - + +
95A VAL* 4.6 6.3 - - + -
110A MET* 3.3 34.5 - - + -
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Residues in contact with GLU 69 (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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65A TYR 3.1 18.9 + - - +
66A THR* 3.4 16.5 + - - +
68A LEU* 1.3 76.9 - - - +
70A ASP* 1.3 66.7 + - - +
73A ASN* 3.1 24.6 + - - +
74A TRP* 3.3 24.0 - - + +
75A TYR 4.7 0.2 - - - -
76A ARG* 2.8 54.8 - - + +
78A LYS* 3.6 14.6 + - - -
95A VAL* 5.6 0.7 - - + -
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Residues in contact with ASP 70 (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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66A THR* 2.9 35.4 + - - +
69A GLU* 1.3 85.1 - - - +
71A THR* 1.3 59.6 + - - +
73A ASN 4.8 0.3 + - - -
207A LYS* 3.7 22.9 + - - +
209A LYS* 4.1 9.8 + - - +
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Residues in contact with THR 71 (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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67A LEU* 2.8 26.2 + - - +
70A ASP* 1.3 75.7 - - - +
72A TYR* 1.3 90.6 + - + +
73A ASN 3.6 0.8 + - - -
209A LYS* 3.4 31.1 + - + +
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Residues in contact with TYR 72 (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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28A GLU* 3.5 58.2 - - + +
31A THR* 3.4 28.3 - - + +
32A SER* 4.9 6.7 - - - -
67A LEU* 3.8 13.9 - - + -
68A LEU* 3.1 19.5 + - + +
71A THR* 1.3 103.9 - - + +
73A ASN* 1.3 72.6 + - - +
74A TRP* 3.3 7.1 + - + -
97A LYS* 3.5 18.4 + - - -
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Residues in contact with ASN 73 (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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68A LEU 3.0 1.8 + - - -
69A GLU 3.1 15.0 + - - +
70A ASP 4.6 0.2 - - - -
71A THR 3.6 1.6 - - - +
72A TYR* 1.3 81.5 - - - +
74A TRP* 1.3 65.7 + - - +
75A TYR* 4.0 0.3 + - - +
97A LYS* 3.8 15.8 - - - +
98A GLU 5.7 0.2 + - - -
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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