Contacts of the helix formed by residues 70 - 84 (chain E) in PDB entry 3V5I
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 70 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E ILE* 2.8 13.9 + - - +
37E ASP* 4.4 6.5 - - - -
38E ASP* 4.4 4.3 + - - -
69E GLY* 1.3 70.5 - - - +
71E VAL* 1.3 58.9 + - - +
72E THR* 3.5 10.0 + - - -
73E ALA* 3.1 30.5 + - - +
74E GLY* 2.9 25.1 + - - -
99E MET* 3.9 3.7 - - - +
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Residues in contact with VAL 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E GLY 3.3 5.3 + - - +
70E SER* 1.3 72.5 + - - +
72E THR* 1.3 63.0 + - + +
74E GLY* 3.3 1.9 + - - -
75E PHE* 3.0 46.7 + - + -
99E MET* 3.6 26.8 - - + +
125E PRO* 4.4 16.2 - - + -
126E LEU 6.1 0.4 - - - +
146E THR* 3.6 27.6 - - + -
150E LEU* 4.3 12.8 - - + -
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Residues in contact with THR 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ASP* 4.7 5.2 + - - -
70E SER* 3.4 8.8 + - - -
71E VAL* 1.3 78.6 - - + +
73E ALA* 1.3 68.5 + - - +
75E PHE* 3.0 7.7 + - + +
76E ALA 3.0 18.2 + - - -
142E HIS* 6.0 1.3 - - + -
65F ASN* 4.8 1.9 + - - -
94F GLY* 3.3 19.1 - - - +
95F MET* 3.8 36.1 - - + +
119F GLU* 3.9 23.6 - - - +
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Residues in contact with ALA 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE* 3.9 8.5 - - + -
37E ASP 3.6 32.5 - - - +
38E ASP* 3.7 10.5 - - - +
41E ALA* 3.5 19.4 - - + +
70E SER* 3.1 24.6 + - - +
72E THR* 1.3 77.8 + - - +
74E GLY* 1.3 62.3 + - - +
76E ALA 3.2 8.5 + - - +
77E ILE* 3.4 10.0 + - - +
65F ASN* 4.5 4.5 - - - +
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Residues in contact with GLY 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE* 3.9 8.7 - - - +
70E SER 2.9 15.0 + - - -
71E VAL 3.3 4.7 + - - -
72E THR 3.2 0.4 - - - -
73E ALA* 1.3 77.8 - - - +
75E PHE* 1.3 56.6 + - - +
77E ILE* 3.1 8.0 + - - +
78E TYR* 2.8 25.2 + - - +
99E MET* 3.7 20.9 - - - -
102E PHE* 5.8 0.2 - - - -
103E LEU* 3.5 12.4 - - - +
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Residues in contact with PHE 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E VAL* 3.0 42.8 + - + +
72E THR* 3.0 9.3 + - + +
74E GLY* 1.3 73.6 - - - +
76E ALA* 1.3 61.9 + - - +
78E TYR* 3.7 15.2 - + + +
79E ASP* 2.7 35.0 + - - +
99E MET* 5.2 1.1 - - - -
102E PHE* 3.8 15.7 - + - -
146E THR* 5.2 0.9 - - + -
149E LYS* 3.5 37.9 - - + -
150E LEU* 3.7 26.0 - - + -
153E ILE* 3.7 23.3 - - + -
94F GLY* 4.6 7.0 - - - +
117F ASN* 3.7 29.8 - - + +
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Residues in contact with ALA 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ALA* 4.5 3.6 - - + -
45E VAL* 4.0 7.0 - - + -
72E THR 3.0 7.7 + - - +
73E ALA 3.5 9.0 - - - +
74E GLY 3.2 0.4 - - - -
75E PHE* 1.3 77.7 - - - +
77E ILE* 1.3 56.3 + - - +
79E ASP* 4.2 1.9 - - - +
80E THR* 2.7 34.2 + - - -
65F ASN* 4.2 11.0 - - - +
93F ILE* 3.9 25.0 - - + +
94F GLY* 3.6 27.5 - - - +
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Residues in contact with ILE 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 5.2 3.6 - - + -
36E ILE* 4.4 13.7 - - + -
40E VAL* 5.2 0.7 - - + -
41E ALA* 3.9 24.5 - - + +
44E ILE* 3.9 44.0 - - + -
45E VAL* 4.2 6.5 - - + -
48E LEU* 4.7 1.3 - - + -
62E LEU* 5.0 3.6 - - + -
73E ALA 3.4 11.4 + - - +
74E GLY 3.1 6.6 + - - +
76E ALA* 1.3 73.4 - - - +
78E TYR* 1.3 66.9 + - - +
80E THR* 3.1 3.4 + - - -
81E ILE* 2.9 42.4 + - + +
103E LEU* 3.9 26.5 - - + -
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Residues in contact with TYR 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E GLY 2.8 19.0 + - - +
75E PHE* 3.2 15.7 + + + +
77E ILE* 1.3 74.9 - - - +
79E ASP* 1.3 77.2 + - - +
81E ILE* 3.2 7.6 + - - +
82E GLN* 3.1 43.6 + - + +
102E PHE* 3.5 20.0 - + + -
103E LEU* 3.7 10.7 - - + +
106E ALA* 3.4 33.2 - - + -
153E ILE* 3.2 33.6 - - + +
156E GLU* 5.2 2.3 + - - -
157E ARG* 3.3 18.8 + - - -
117F ASN* 3.6 18.8 - - - -
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Residues in contact with ASP 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E PHE 2.7 21.1 + - - +
76E ALA* 4.3 2.2 - - - +
78E TYR* 1.3 84.0 - - - +
80E THR* 1.3 56.0 + - - +
82E GLN* 3.3 6.3 + - - +
83E HIS* 2.8 30.1 + - - +
93F ILE* 5.9 0.4 - - + -
94F GLY 5.7 1.4 + - - +
115F LEU* 3.4 25.9 - - + +
116F PRO* 3.4 18.0 - - + +
117F ASN* 2.6 57.0 + - - +
118F ALA* 3.5 4.3 + - - +
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Residues in contact with THR 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E VAL* 3.5 31.1 - - + +
48E LEU* 3.8 28.9 - - + -
49E LEU* 4.5 8.5 - - + -
76E ALA 2.7 22.4 + - - -
77E ILE 3.1 4.8 + - - -
79E ASP* 1.3 73.2 - - - +
81E ILE* 1.3 68.5 + - - +
83E HIS* 3.2 3.8 + - + +
84E ILE* 3.1 30.1 + - + +
63F TYR* 6.1 0.2 - - - -
93F ILE* 4.4 4.7 - - - +
115F LEU* 4.2 12.7 - - - +
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Residues in contact with ILE 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E LEU* 3.9 16.2 - - + -
62E LEU* 4.1 20.9 - - + -
77E ILE* 2.9 36.5 + - + +
78E TYR* 3.6 9.6 - - - +
80E THR* 1.3 78.5 - - - +
82E GLN* 1.3 69.4 + - - +
83E HIS 3.2 0.3 + - - -
84E ILE* 3.4 22.0 + - - +
86E PRO 4.8 1.9 - - - +
88E VAL* 3.8 33.2 - - + +
90E THR* 5.4 2.0 - - + -
103E LEU* 4.8 8.7 - - + +
106E ALA* 3.9 27.8 - - + +
107E GLY* 5.1 0.7 - - - -
108E ALA 5.5 0.9 - - - +
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Residues in contact with GLN 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TYR* 3.1 51.6 + - + +
79E ASP* 3.8 6.3 - - - +
81E ILE* 1.3 81.7 - - - +
83E HIS* 1.3 59.8 + - - +
84E ILE 3.6 4.9 + - - +
106E ALA* 3.2 24.6 + - - +
107E GLY 6.0 0.2 - - - -
108E ALA* 6.3 0.2 - - - +
157E ARG* 3.6 20.9 + - - +
192F PRO* 3.9 29.9 - - + +
193F GLU 4.2 5.9 + - - -
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Residues in contact with HIS 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LEU* 5.3 6.1 - - + +
52E GLN* 4.5 4.4 + - - -
79E ASP 2.8 18.5 + - - +
80E THR* 3.2 5.7 + - - +
82E GLN* 1.3 78.8 - - - +
84E ILE* 1.3 69.8 + - - +
63F TYR* 5.4 5.4 - - - -
115F LEU* 4.3 11.5 - - + +
116F PRO* 6.3 1.3 - - + -
190F MET* 3.1 54.8 - - + +
191F VAL 4.5 9.4 - - - -
192F PRO* 4.7 3.8 - - + -
193F GLU* 3.9 33.5 + - + +
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Residues in contact with ILE 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E LEU* 4.2 19.7 - - + +
49E LEU* 4.2 19.5 - - + -
52E GLN* 3.3 30.3 - - + +
60E ILE* 3.8 28.9 - - + -
80E THR* 3.3 21.8 - - + +
81E ILE 3.4 15.1 - - - +
82E GLN 3.8 4.9 - - - +
83E HIS* 1.3 86.0 - - - +
85E LYS* 1.3 66.0 + - - +
86E PRO* 3.8 14.3 - - + +
88E VAL* 4.0 15.3 - - + -
193F GLU* 5.5 3.4 - - - -
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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