Contacts of the helix formed by residues 58 - 72 (chain H) in PDB entry 3EXF
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 58 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E ASN* 2.9 29.6 + - - +
172E GLN* 4.9 0.4 - - - +
177G GLU* 3.2 27.9 + - - +
180G ASN* 5.1 0.5 + - - -
181G MET* 3.5 23.3 - - - +
56H PRO* 3.0 13.0 + - - +
57H ILE* 1.3 75.5 + - - +
59H GLU* 1.3 59.8 + - - +
61H GLY 3.3 0.3 + - - -
62H PHE* 2.9 31.9 + - - -
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Residues in contact with GLU 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E GLN* 3.4 19.8 + - - -
1009E TPP 2.5 36.8 + - - -
177G GLU* 4.0 0.4 + - - -
28H GLU* 2.8 18.8 - - - +
57H ILE 3.6 4.5 - - - +
58H SER* 1.3 66.7 - - - +
60H MET* 1.3 71.3 + - - +
61H GLY 3.0 0.2 + - - -
62H PHE* 3.7 16.5 - - + -
63H ALA* 2.9 29.7 + - - +
80H PHE* 4.5 7.4 - - + -
81H MET 5.6 1.4 + - - -
85H PHE* 3.4 27.6 - - + +
88H GLN* 3.3 20.8 - - + +
89H ALA* 4.2 5.8 - - + -
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Residues in contact with MET 60 (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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60F MET* 5.8 2.7 - - + -
88F GLN* 3.8 46.2 - - + +
143G PRO* 4.5 1.7 - - - +
174G GLN* 3.5 36.1 - - + +
177G GLU* 3.7 12.8 + - - +
58H SER 3.6 0.2 - - - -
59H GLU* 1.3 78.9 - - - +
61H GLY* 1.3 65.1 + - - +
63H ALA* 3.4 2.9 - - - +
64H GLY* 3.3 11.1 + - - -
88H GLN* 2.7 42.6 - - + +
89H ALA* 4.1 7.6 - - - +
91H ASP* 4.2 9.6 - - + +
92H GLN* 3.9 30.0 - - - +
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Residues in contact with GLY 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G PRO* 3.5 16.8 - - - +
174G GLN 5.0 1.1 - - - -
177G GLU* 2.5 29.2 + - - -
178G ALA* 5.2 0.9 - - - -
181G MET* 3.9 14.6 - - - -
58H SER 3.5 0.9 - - - -
59H GLU 3.0 1.4 + - - -
60H MET* 1.3 73.0 - - - +
62H PHE* 1.3 51.5 + - - -
64H GLY* 2.6 26.3 + - - -
65H ILE* 2.9 12.1 + - - +
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Residues in contact with PHE 62 (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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181G MET* 3.8 18.6 - - - +
26H LEU* 4.3 22.8 - - + +
27H GLY* 4.6 3.4 - - - -
28H GLU* 4.1 21.3 - - + -
55H THR* 3.4 26.0 - - + -
56H PRO 4.0 3.6 - - - -
58H SER* 2.9 35.4 + - - +
59H GLU* 3.7 17.7 - - + -
61H GLY* 1.3 67.7 - - - -
63H ALA* 1.3 70.4 + - - +
65H ILE* 3.8 10.3 - - + +
66H ALA* 2.8 25.3 + - - +
78H CYS* 3.7 24.9 - - - -
79H GLU 3.9 23.1 - - - -
80H PHE* 4.3 13.5 - + - -
81H MET 5.9 0.2 - - - -
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Residues in contact with ALA 63 (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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59H GLU 2.9 20.5 + - - +
60H MET 3.4 5.4 - - - +
62H PHE* 1.3 87.9 - - - +
64H GLY* 1.3 58.1 + - - +
66H ALA* 3.0 3.1 + - - +
67H VAL* 2.9 30.2 + - - +
78H CYS* 4.2 10.1 - - - -
80H PHE* 4.3 6.5 - - + -
89H ALA* 3.5 24.9 - - + +
92H GLN* 4.2 10.5 - - + -
93H VAL* 5.7 0.2 - - + -
114H PHE* 4.7 5.7 - - + -
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Residues in contact with GLY 64 (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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143G PRO* 3.6 22.0 - - - +
144G LEU* 3.5 9.1 - - - +
60H MET 3.3 1.4 + - - -
61H GLY 2.6 15.5 + - - -
63H ALA* 1.3 72.7 - - - +
65H ILE* 1.3 65.0 + - - +
67H VAL* 3.3 4.1 + - - -
68H GLY 3.0 15.6 + - - -
92H GLN* 3.8 22.2 - - - -
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Residues in contact with ILE 65 (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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143G PRO* 3.2 8.1 + - + +
146G ALA* 3.4 35.4 - - + +
147G GLY* 3.1 21.9 - - - +
150G LEU* 4.2 20.6 - - + -
178G ALA* 5.0 4.9 - - + -
181G MET* 3.6 43.3 - - + -
185G TRP* 4.2 11.2 - - + -
187G LEU* 5.0 3.4 - - + -
26H LEU* 4.2 13.0 - - + -
61H GLY 2.9 9.4 + - - +
62H PHE* 3.8 8.3 - - - +
63H ALA 3.4 0.2 - - - -
64H GLY* 1.3 75.4 - - - +
66H ALA* 1.3 69.0 + - - +
68H GLY 2.9 11.6 + - - -
69H ALA* 3.1 3.5 + - - +
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Residues in contact with ALA 66 (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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24H PHE* 5.5 1.8 - - - -
26H LEU* 3.8 24.7 - - + -
62H PHE 2.8 22.3 + - - +
63H ALA 3.3 3.8 - - - +
65H ILE* 1.3 77.2 - - - +
67H VAL* 1.3 63.8 + - - +
69H ALA* 3.5 6.2 + - - +
70H ALA* 3.0 21.0 + - - +
76H PRO* 3.6 11.5 - - + +
78H CYS* 3.9 8.3 - - + -
112H ILE* 3.7 16.6 - - + -
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Residues in contact with VAL 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G LEU* 3.7 16.8 - - + -
63H ALA 2.9 18.6 + - - +
64H GLY* 3.7 7.9 - - - +
66H ALA* 1.3 75.3 - - - +
68H GLY* 1.3 55.6 + - - +
70H ALA* 3.3 5.0 + - - +
71H MET* 2.9 37.6 + - + +
92H GLN* 4.3 15.5 - - + +
96H SER* 4.3 3.6 - - - -
97H ALA* 3.9 28.7 - - + +
110H VAL* 4.0 11.0 - - + -
112H ILE* 3.6 16.8 - - + +
114H PHE* 4.2 13.0 - - + -
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Residues in contact with GLY 68 (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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144G LEU* 3.6 24.8 - - - +
147G GLY 3.6 7.0 - - - -
148G ILE* 3.8 6.6 - - - +
64H GLY 3.0 6.4 + - - -
65H ILE 2.9 9.9 + - - -
67H VAL* 1.3 72.5 - - - +
69H ALA* 1.3 63.0 + - - -
70H ALA 3.1 0.9 - - - -
71H MET* 3.0 12.1 + - - +
72H ALA* 2.9 24.1 + - - +
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Residues in contact with ALA 69 (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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147G GLY 3.1 20.3 + - - +
150G LEU* 4.4 7.2 - - + -
151G ALA* 4.4 8.1 - - + -
24H PHE* 4.0 31.6 - - + -
65H ILE 3.1 7.0 + - - +
66H ALA* 3.6 9.0 - - - +
68H GLY* 1.3 71.8 - - - +
70H ALA* 1.3 64.2 + - - +
72H ALA 3.1 10.2 + - - -
74H LEU* 3.0 31.3 + - + +
76H PRO* 5.1 0.7 - - + -
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Residues in contact with ALA 70 (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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66H ALA 3.0 14.2 + - - +
67H VAL* 3.3 14.4 - - - +
68H GLY 3.1 0.2 - - - -
69H ALA* 1.3 75.4 - - - +
71H MET* 1.3 63.0 + - - +
73H GLY* 3.1 11.8 + - - -
74H LEU 3.4 12.9 - - - +
76H PRO* 3.6 20.8 - - + +
109H PRO 4.4 0.5 - - - +
110H VAL* 4.2 7.2 - - + -
111H PRO* 3.6 20.8 - - - +
112H ILE* 4.0 18.8 - - + +
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Residues in contact with MET 71 (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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86G ILE* 4.6 0.4 - - + -
127G TYR* 5.3 3.1 - - + -
132G TYR* 3.9 37.1 - - + +
135G ASN* 5.1 1.1 - - - +
144G LEU* 3.7 32.8 - - + -
148G ILE* 4.5 8.7 - - + -
67H VAL* 2.9 35.1 + - + +
68H GLY* 3.0 7.8 + - - +
70H ALA* 1.3 75.7 - - - +
72H ALA* 1.3 57.4 - - - +
73H GLY 3.2 4.5 + - - -
96H SER* 5.2 1.8 - - - +
100H THR* 4.3 15.9 - - - -
108H GLN* 3.1 54.0 + - + +
109H PRO* 4.4 2.8 - - - +
110H VAL* 4.6 7.9 - - + -
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Residues in contact with ALA 72 (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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84G HIS* 5.7 2.9 - - + -
132G TYR* 3.7 22.2 - - + +
148G ILE* 4.3 11.9 - - + -
151G ALA* 4.2 18.5 - - + +
155G ASN* 4.9 3.5 + - - -
68H GLY 2.9 14.0 + - - +
69H ALA 3.1 6.4 + - - +
71H MET* 1.3 75.0 - - - +
73H GLY* 1.3 60.2 + - - -
74H LEU* 3.4 8.0 + - - +
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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
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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