Contacts of the helix formed by residues 62 - 84 (chain E) in PDB entry 3P05
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 HIS 62 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ASP* 3.7 17.5 + - - +
27E VAL* 4.1 18.7 + - + -
28E GLU* 4.4 7.7 + - - -
31E ALA* 4.0 32.4 - - + -
32E PHE* 3.7 24.4 - + + -
59E VAL* 4.6 4.0 - - + -
60E GLY 3.7 15.7 - - - -
61E GLY* 1.3 70.5 - - - +
63E GLN* 1.3 58.7 + - - +
64E ALA 3.2 2.9 - - - -
65E ALA* 3.2 3.2 + - + -
66E MET* 2.9 27.5 + - - +
145E TYR* 2.9 29.5 + + - +
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Residues in contact with GLN 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ASP* 3.3 11.1 + - - +
169D TYR* 3.6 26.9 - - + +
170D LYS* 4.0 17.9 - - + +
173D ARG* 3.8 29.8 + - - +
233D IOD 3.8 27.6 - - + +
59E VAL 3.8 5.7 + - - -
61E GLY* 2.8 25.8 + - - +
62E HIS* 1.3 74.7 - - - +
64E ALA* 1.3 61.1 + - - +
66E MET* 3.7 22.9 - - - +
67E GLN* 2.9 32.7 + - - +
70E LYS* 5.8 1.6 + - - -
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ARG* 4.4 4.3 - - + -
165D VAL* 3.7 24.2 - - + -
166D ASP* 2.7 27.2 + - - +
211D LEU* 3.8 2.1 - - - +
215D MET* 3.7 33.0 - - + -
63E GLN* 1.3 72.8 - - - +
65E ALA* 1.3 57.4 + - - +
67E GLN* 3.3 4.7 + - - +
68E MET* 2.9 34.2 + - + +
145E TYR* 6.0 1.1 - - + +
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Residues in contact with ALA 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ASP* 4.5 0.2 + - - -
32E PHE* 3.8 19.1 - - + -
62E HIS* 3.2 11.0 + - + +
64E ALA* 1.3 77.5 - - - +
66E MET* 1.3 60.6 + - - +
68E MET* 3.2 10.9 + - + +
69E LEU* 2.9 29.6 + - - +
141E ILE* 3.4 37.3 - - + +
145E TYR* 4.3 12.2 + - + +
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Residues in contact with MET 66 (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 PHE* 4.4 15.5 - - - -
56E LEU* 3.6 37.9 - - + +
59E VAL* 4.0 28.3 - - + -
62E HIS 2.9 22.4 + - - +
63E GLN* 3.4 30.7 + - - +
65E ALA* 1.3 76.0 - - - +
67E GLN* 1.3 57.8 + - - +
69E LEU* 3.3 28.1 + - + +
70E LYS* 3.0 38.2 + - - +
141E ILE* 5.7 0.2 - - - -
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Residues in contact with GLN 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D TYR* 3.7 39.4 + - + +
179D GLN* 4.2 19.7 + - - +
182D LYS* 6.0 3.0 - - - +
183D ASN* 5.1 4.2 + - - -
211D LEU* 3.7 20.4 - - + -
63E GLN* 2.9 19.4 + - - +
64E ALA 3.4 4.3 - - - +
66E MET* 1.3 78.2 - - - +
68E MET* 1.3 61.1 + - - +
70E LYS* 3.2 27.2 + - - +
71E GLU* 3.1 30.8 + - - +
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Residues in contact with MET 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 4.1 10.0 - - + +
212D GLU* 3.9 37.0 - - + +
215D MET* 3.8 26.0 - - + -
64E ALA 2.9 14.1 + - - +
65E ALA* 3.2 22.6 + - + +
67E GLN* 1.3 69.8 - - - +
69E LEU* 1.3 66.2 + - - +
71E GLU* 3.2 11.6 + - - +
72E THR* 3.0 26.9 + - - +
140E LYS* 6.1 2.7 - - - -
141E ILE* 4.8 18.8 - - + -
144E MET* 3.8 35.2 - - + +
145E TYR* 5.6 4.7 - - + -
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Residues in contact with LEU 69 (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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56E LEU* 3.9 20.6 - - + -
65E ALA 2.9 16.0 + - - +
66E MET* 3.4 32.5 - - + +
68E MET* 1.3 76.6 - - - +
70E LYS* 1.3 57.9 + - - +
72E THR* 3.2 5.3 + - - -
73E ILE* 2.9 44.1 + - + +
133E TRP 4.7 0.4 - - - +
134E ILE* 3.7 27.8 - - + +
137E GLY* 3.8 17.7 - - - -
138E LEU* 4.3 18.6 - - + -
141E ILE* 4.0 8.9 - - + +
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Residues in contact with LYS 70 (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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179D GLN* 4.2 21.9 + - - +
57E ASN* 5.2 7.4 + - - -
63E GLN* 5.8 1.8 + - - -
66E MET* 3.0 18.6 + - - +
67E GLN* 3.3 35.4 + - - +
69E LEU* 1.3 77.1 - - - +
71E GLU* 1.3 57.1 + - + +
73E ILE* 3.2 12.7 + - + +
74E ASN* 2.8 45.0 + - - +
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Residues in contact with GLU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D THR* 3.6 16.1 - - - +
211D LEU* 3.2 43.6 + - - +
212D GLU* 4.3 3.1 + - - +
67E GLN* 3.1 23.2 + - - +
68E MET* 3.2 10.0 + - - +
70E LYS* 1.3 76.7 - - + +
72E THR* 1.3 56.3 + - - +
74E ASN* 3.2 12.1 + - - +
75E GLU* 2.9 40.6 + - + +
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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
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68E MET* 3.0 14.6 + - - +
69E LEU* 3.2 8.0 + - - -
71E GLU* 1.3 72.8 - - - +
73E ILE* 1.3 66.8 + - - +
75E GLU* 3.4 10.8 + - - +
76E GLU* 3.0 31.8 + - + +
133E TRP 4.2 5.4 - - - +
136E LEU* 4.0 19.7 - - + -
137E GLY* 3.8 30.9 - - - +
140E LYS* 2.9 32.9 + - - +
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Residues in contact with ILE 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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56E LEU* 4.3 6.7 - - + -
69E LEU* 2.9 42.7 + - + +
70E LYS* 3.6 10.8 - - + +
72E THR* 1.3 77.0 - - - +
74E ASN* 1.3 70.0 + - - +
76E GLU* 3.1 6.8 + - - +
77E ALA* 2.9 24.2 + - + +
105E ALA* 3.8 28.5 - - + -
130E TYR* 3.9 30.3 - - + +
133E TRP* 4.3 15.3 - - + +
134E ILE* 4.1 13.2 - - + -
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Residues in contact with ASN 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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179D GLN* 5.6 4.6 - - - +
70E LYS* 2.8 32.2 + - - +
71E GLU* 3.5 13.1 - - - +
73E ILE* 1.3 81.9 - - - +
75E GLU* 1.3 62.0 + - + +
77E ALA* 3.4 7.0 + - - +
78E ALA* 3.1 23.8 + - - +
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Residues in contact with GLU 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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210D THR* 4.7 15.8 - - - +
212D GLU* 5.7 0.5 - - - +
71E GLU* 2.9 33.8 + - + +
72E THR* 3.8 9.6 + - - +
73E ILE 3.3 0.2 - - - -
74E ASN* 1.3 73.0 - - + +
76E GLU* 1.3 65.8 + - - +
78E ALA* 3.7 5.7 + - - +
79E GLU* 3.1 26.3 + - - +
140E LYS* 3.9 18.5 + - - -
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Residues in contact with GLU 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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72E THR* 3.0 20.8 + - + +
73E ILE 3.8 1.3 - - - +
75E GLU* 1.3 83.7 - - - +
77E ALA* 1.3 61.4 + - - +
79E GLU* 3.4 14.2 + - - +
80E TRP* 2.9 27.4 + - - +
133E TRP* 3.6 44.5 + - + -
136E LEU* 3.4 34.1 - - + +
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Residues in contact with ALA 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ILE* 2.9 18.5 + - + +
74E ASN* 3.7 7.6 - - - +
76E GLU* 1.3 75.4 - - - +
78E ALA* 1.3 65.4 + - - +
80E TRP* 3.0 4.3 + - - +
81E ASP* 3.0 27.3 + - - +
101E GLY* 3.8 24.5 - - - -
102E SER* 4.3 3.4 - - - +
105E ALA* 5.4 1.8 - - + -
133E TRP* 3.7 17.2 - - + -
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Residues in contact with ALA 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 ASN 3.1 15.2 + - - +
75E GLU* 3.9 7.0 - - - +
77E ALA* 1.3 78.2 - - - +
79E GLU* 1.3 62.4 + - - +
81E ASP* 3.2 12.2 + - - +
82E ARG* 3.1 26.3 + - - +
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Residues in contact with GLU 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 GLU 3.1 18.6 + - - +
76E GLU* 3.6 17.3 - - - +
77E ALA 3.2 0.2 - - - -
78E ALA* 1.3 79.0 - - - +
80E TRP* 1.3 60.9 + - - +
82E ARG* 2.4 38.9 + - - +
83E LEU* 3.3 41.3 + - + +
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Residues in contact with TRP 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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76E GLU 2.9 14.4 + - - +
77E ALA 3.0 8.5 + - - +
79E GLU* 1.3 73.6 - - - +
81E ASP* 1.3 76.9 + - - +
83E LEU* 3.1 4.9 + - - -
84E HIS* 2.9 74.5 + + + +
99E PRO* 3.3 30.6 + - + -
100E ARG* 4.3 0.2 - - - +
101E GLY* 3.6 11.9 - - - -
104E ILE* 3.3 25.2 - - + +
124E ILE* 5.2 6.5 - - + -
129E ILE* 4.2 28.3 - - + -
133E TRP* 3.8 17.9 - + + -
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Residues in contact with ASP 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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77E ALA* 3.0 15.8 + - - +
78E ALA* 3.4 11.9 - - - +
80E TRP* 1.3 80.4 - - - +
82E ARG* 1.3 62.8 + - - +
83E LEU 3.1 1.0 + - - -
84E HIS 3.1 22.8 + - - +
85E PRO* 3.3 11.7 - - + +
100E ARG* 3.6 12.4 - - - +
101E GLY* 2.8 30.0 + - - -
102E SER 5.0 1.2 + - - -
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Residues in contact with ARG 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 ALA* 3.1 16.4 + - + +
79E GLU* 2.4 43.8 + - - +
81E ASP* 1.3 75.0 - - - +
83E LEU* 1.3 79.3 + - - +
85E PRO* 4.6 6.2 - - - +
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Residues in contact with LEU 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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79E GLU* 3.3 29.6 - - + +
80E TRP* 3.1 5.5 + - - +
82E ARG* 1.3 112.3 - - - +
84E HIS* 1.3 85.8 + - + +
85E PRO* 3.9 5.0 - - - +
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Residues in contact with HIS 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E TRP* 2.9 66.4 + + + +
81E ASP* 3.1 11.4 + - - +
83E LEU* 1.3 99.3 + - + +
85E PRO* 1.3 67.6 - - - +
98E GLU* 5.1 4.0 - - - +
99E PRO 5.1 3.4 - - - +
100E ARG* 5.7 1.4 - - - -
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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
------------------------------------------------------------
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