Contacts of the helix formed by residues 67 - 79 (chain E) in PDB entry 2POZ
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 ARG 67 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLY 3.8 3.6 - - - -
118A GLY* 4.6 0.9 - - - -
119A LYS* 3.4 55.2 + - - +
120A ILE 3.5 12.3 + - - -
121A ARG* 4.8 0.4 - - - +
122A ASP* 3.7 15.4 + - - -
64E ASP* 3.4 24.9 + - - +
65E PRO 3.2 1.8 - - - -
66E SER* 1.3 82.7 - - - +
68E ILE* 1.3 56.7 + - - +
69E GLU 3.5 2.2 - - - -
70E GLU* 2.8 49.8 + - + +
71E LEU* 2.9 35.5 + - + +
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Residues in contact with ILE 68 (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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117A GLY* 3.2 8.6 + - - +
65E PRO 3.4 16.6 - - - +
66E SER 3.0 8.2 + - - +
67E ARG* 1.3 70.9 - - - +
69E GLU* 1.3 65.9 + - + +
71E LEU* 3.1 9.7 + - - +
72E TRP* 2.9 24.4 + - + +
97E GLU* 4.2 16.8 - - + -
100E LEU* 3.7 37.6 - - + +
101E TRP* 3.6 45.3 - - + +
104E LYS* 3.6 22.0 - - - -
288E MSE 6.1 0.2 - - + -
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Residues in contact with GLU 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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116A PHE 3.8 8.9 - - - +
117A GLY* 3.1 13.5 + - - +
118A GLY 4.8 0.4 - - - +
120A ILE* 4.1 8.5 - - + -
291A LYS* 3.0 19.7 + - - -
324A ASN* 3.5 37.3 - - - +
325A ILE* 5.5 0.2 - - - -
326A THR* 3.6 22.2 + - - +
68E ILE* 1.3 76.8 - - + +
70E GLU* 1.3 57.9 + - - +
72E TRP* 3.7 6.5 - - - +
73E SER* 2.9 30.8 + - - -
101E TRP* 5.6 1.2 - - + -
288E MSE 3.9 8.3 - - - +
292E LYS* 2.9 31.7 + - - -
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Residues in contact with GLU 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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117A GLY 4.9 0.2 + - - -
119A LYS 4.2 1.3 + - - +
120A ILE* 3.3 29.7 - - + +
174D ARG* 4.3 18.5 + - - +
67E ARG* 2.8 56.8 + - + +
68E ILE 3.2 0.4 - - - -
69E GLU* 1.3 75.7 - - - +
71E LEU* 1.3 64.0 + - + +
73E SER* 3.6 5.7 - - - -
74E THR* 2.6 45.6 + - - +
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Residues in contact with LEU 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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5E ILE* 5.4 0.9 - - + -
59E PHE* 4.4 11.2 - - + +
60E LEU* 4.4 14.4 - - + -
63E LYS* 4.4 24.7 - - + +
64E ASP 3.6 21.1 - - - +
65E PRO* 4.2 8.5 - - + +
67E ARG* 2.9 28.1 + - + +
68E ILE 3.1 5.4 + - - +
70E GLU* 1.3 79.5 - - - +
72E TRP* 1.3 65.0 + - - +
74E THR* 3.1 9.6 + - + +
75E MSE 2.9 36.1 + - + +
100E LEU* 3.8 28.7 - - + -
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Residues in contact with TRP 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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326A THR* 6.5 0.4 - - + -
68E ILE* 2.9 16.3 + - + +
69E GLU* 3.7 7.9 - - - +
71E LEU* 1.3 76.0 - - - +
73E SER* 1.3 63.8 + - - +
75E MSE 3.3 12.7 + - + +
76E TYR* 2.9 59.3 + + + -
90E PHE* 4.2 19.3 - + - -
93E ILE* 3.4 23.2 - - + +
97E GLU* 3.9 21.8 - - + -
100E LEU* 5.7 0.2 - - - +
261E THR* 4.4 5.8 - - + -
262E ARG* 4.0 17.5 - - - -
263E PHE* 4.8 7.2 - + - -
285E GLY* 2.8 25.9 + - - -
289E GLU* 3.6 36.5 - - + +
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Residues in contact with SER 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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326A THR* 3.9 17.4 - - - +
174D ARG* 3.3 36.2 + - - +
69E GLU 2.9 19.3 + - - -
70E GLU* 3.6 7.6 - - - -
72E TRP* 1.3 85.6 - - - +
74E THR* 1.3 56.7 + - - +
76E TYR* 3.6 2.7 - - - +
77E ASP* 2.9 34.9 + - - +
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Residues in contact with THR 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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174D ARG* 5.0 4.4 + - - +
58E ARG* 5.8 0.4 - - - +
59E PHE* 3.7 26.4 - - + -
63E LYS* 6.0 4.0 - - - +
70E GLU* 2.6 37.2 + - - +
71E LEU* 3.1 11.2 + - + +
73E SER* 1.3 71.4 + - - +
75E MSE 1.3 61.2 + - - +
77E ASP* 4.6 0.4 - - - -
78E HIS* 2.9 47.0 + - + +
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Residues in contact with MSE 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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55E LEU* 4.5 11.0 - - + -
59E PHE* 3.6 37.0 - - + -
60E LEU* 4.9 4.3 - - + -
71E LEU* 2.9 29.1 + - + +
72E TRP* 3.7 13.2 - - + +
74E THR* 1.3 75.7 - - - +
76E TYR* 1.3 60.2 + - - +
79E SER* 2.9 32.4 + - - -
82E ALA* 4.1 0.3 - - - +
93E ILE* 3.9 43.2 - - + +
96E ILE* 3.8 44.2 - - + -
97E GLU* 5.1 2.2 - - + +
100E LEU* 5.2 2.7 - - + -
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Residues in contact with TYR 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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175D ARG* 4.9 5.2 - - - -
235D ASP* 2.4 37.8 + - - -
237D PHE* 3.5 12.8 - + - -
72E TRP* 2.9 42.0 + + + +
73E SER* 3.6 4.9 - - - +
75E MSE 1.3 78.9 - - - +
77E ASP* 1.3 76.8 + - - +
78E HIS 3.5 0.2 + - - -
79E SER* 3.9 2.4 + - - -
80E PHE 4.6 1.7 + - - -
82E ALA* 3.5 43.7 - - + +
83E LYS* 3.7 24.2 - - + +
90E PHE* 3.9 15.3 - + - -
93E ILE* 4.7 3.5 - - + +
263E PHE* 3.8 27.2 - + - -
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Residues in contact with ASP 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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171D HIS* 5.2 4.3 - - - +
172D VAL 4.2 7.9 - - - +
173D THR* 3.6 5.2 - - - +
174D ARG* 2.6 44.9 + - - +
175D ARG* 6.1 0.7 - - - +
73E SER* 2.9 22.0 + - - +
74E THR* 4.6 0.4 - - - -
76E TYR* 1.3 94.4 - - - +
78E HIS* 1.3 85.8 + - + +
79E SER 4.1 0.2 + - - -
80E PHE* 4.6 3.3 + - - -
83E LYS* 4.1 21.8 + - - +
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Residues in contact with HIS 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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42D GLY* 5.2 2.3 - - - -
43D VAL* 4.1 5.4 - - - +
170D GLN* 3.5 29.4 + - + +
171D HIS 3.4 30.7 + - - -
172D VAL 4.0 3.1 - - - -
173D THR* 3.2 22.6 + - - +
58E ARG* 4.8 11.1 + - - +
59E PHE* 3.7 21.3 - - + -
74E THR* 2.9 31.8 + - + +
77E ASP* 1.3 99.7 + - + +
79E SER* 1.3 61.8 + - - +
80E PHE* 3.2 3.0 - - - +
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Residues in contact with SER 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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42D GLY* 3.4 0.6 - - - -
43D VAL* 2.8 44.3 + - - -
55E LEU* 4.4 1.3 - - - -
59E PHE* 4.0 6.7 - - - -
75E MSE 2.9 21.1 + - - -
77E ASP 3.7 0.4 - - - -
78E HIS* 1.3 78.5 - - - +
80E PHE* 1.3 62.4 + - - +
81E TRP* 2.9 9.6 + - - -
82E ALA* 3.1 28.1 + - - +
89E ILE* 4.0 17.5 - - - +
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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