Contacts of the helix formed by residues 67 - 79 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LYS* 5.7 3.0 - - - +
64A ASP* 3.4 34.9 + - - +
65A PRO 3.2 2.7 - - - -
66A SER* 1.3 81.4 + - - +
68A ILE* 1.3 61.9 + - - +
69A GLU 3.5 2.2 - - - -
70A GLU* 2.8 40.5 + - + -
71A LEU* 2.6 44.6 + - + +
114E GLU* 6.2 0.2 - - - +
117E GLY 4.0 2.7 - - - -
118E GLY* 4.4 0.9 - - - -
119E LYS* 3.4 37.0 - - + +
120E ILE 6.0 0.7 - - - -
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Residues in contact with ILE 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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65A PRO 3.5 17.0 - - - +
66A SER 3.0 6.7 + - - +
67A ARG* 1.3 68.6 - - - +
69A GLU* 1.3 68.6 + - + +
71A LEU* 3.2 2.8 + - - +
72A TRP* 2.9 23.5 + - + +
97A GLU* 4.2 13.9 - - + +
100A LEU* 3.7 43.0 - - + +
101A TRP* 3.5 48.2 - - + +
104A LYS* 3.5 20.6 - - + -
288A MSE 6.0 0.4 - - + -
117E GLY* 3.0 12.2 + - - +
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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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68A ILE* 1.3 78.3 - - + +
70A GLU* 1.3 57.9 + - - +
72A TRP* 3.4 8.1 + - - +
73A SER* 3.0 30.0 + - - -
101A TRP* 5.9 0.4 - - + -
288A MSE 3.9 8.8 - - + +
292A LYS* 2.8 35.1 + - - -
116E PHE 3.9 7.4 - - - +
117E GLY* 3.0 12.6 + - - +
118E GLY 4.8 0.4 - - - +
120E ILE* 4.0 18.2 - - + -
291E LYS* 2.8 21.4 + - - -
324E ASN* 3.6 28.5 - - - +
326E THR* 3.7 17.9 + - - +
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Residues in contact with GLU 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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67A ARG* 2.8 57.8 + - + +
68A ILE 3.2 0.6 - - - -
69A GLU* 1.3 80.3 - - - +
71A LEU* 1.3 61.5 + - + +
73A SER* 3.3 4.8 + - - -
74A THR* 2.8 40.4 + - - +
118E GLY 6.2 0.2 - - - -
119E LYS 4.3 1.1 + - - +
120E ILE* 3.4 43.2 - - + +
174F ARG* 4.3 15.0 + - - +
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Residues in contact with LEU 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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5A ILE* 5.8 1.3 - - + -
59A PHE* 3.9 10.1 - - + +
60A LEU* 4.1 14.6 - - + -
63A LYS* 3.3 42.4 - - + +
64A ASP 3.8 18.8 - - - +
65A PRO* 5.3 0.9 - - + -
67A ARG* 2.6 41.9 + - + +
68A ILE 3.2 4.0 + - - +
70A GLU* 1.3 78.9 - - + +
72A TRP* 1.3 66.3 + - - +
74A THR* 3.3 4.4 + - - +
75A MSE 3.1 34.5 + - + +
100A LEU* 4.2 24.0 - - + -
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Residues in contact with TRP 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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68A ILE* 2.9 17.2 + - + +
69A GLU* 3.7 10.1 - - - +
71A LEU* 1.3 75.7 - - - +
73A SER* 1.3 69.8 + - - +
75A MSE 3.2 13.2 + - + +
76A TYR* 2.9 56.3 + + + +
90A PHE* 4.2 19.7 - + - -
93A ILE* 3.2 21.9 - - + +
97A GLU* 3.9 21.5 - - + -
100A LEU* 5.7 0.2 - - - +
261A THR* 4.5 5.6 - - + -
262A ARG* 4.1 17.3 - - - -
263A PHE* 5.0 4.5 - + - -
285A GLY* 2.9 27.7 + - - -
289A GLU* 3.9 35.7 - - + +
326E THR* 6.5 0.7 - - + -
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Residues in contact with SER 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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69A GLU 3.0 17.7 + - - -
70A GLU* 3.5 5.4 - - - -
72A TRP* 1.3 86.6 - - - +
74A THR* 1.3 56.2 + - - +
76A TYR* 3.3 3.0 + - - +
77A ASP* 2.8 41.6 + - - +
326E THR* 4.1 16.9 - - - +
174F ARG* 3.1 38.7 + - - +
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Residues in contact with THR 74 (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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59A PHE* 3.6 27.5 - - + -
63A LYS* 3.8 17.5 + - - +
70A GLU* 2.8 32.7 + - - +
71A LEU* 3.6 9.0 - - - +
72A TRP 3.2 0.2 - - - -
73A SER* 1.3 75.9 - - - +
75A MSE 1.3 59.0 + - - +
77A ASP* 4.6 0.7 - - - -
78A HIS* 2.9 47.3 + - + +
174F ARG* 5.1 3.8 + - - +
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Residues in contact with MSE 75 (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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55A LEU* 4.1 16.6 - - + -
59A PHE* 3.8 31.2 - - + -
60A LEU* 4.7 7.2 - - + -
71A LEU* 3.1 27.3 + - + +
72A TRP* 3.7 11.9 - - + +
74A THR* 1.3 73.0 - - - +
76A TYR* 1.3 60.1 + - - +
79A SER* 2.7 36.6 + - - -
82A ALA* 4.1 0.3 - - - +
93A ILE* 4.0 39.8 - - + +
96A ILE* 3.8 47.1 - - + -
97A GLU* 5.1 2.0 - - + +
100A LEU* 5.3 2.0 - - + -
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Residues in contact with TYR 76 (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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72A TRP* 2.9 47.3 + + + +
73A SER* 3.6 5.6 - - - +
75A MSE 1.3 81.1 - - - +
77A ASP* 1.3 75.7 + - - +
78A HIS 3.6 0.2 + - - -
79A SER* 3.7 2.6 + - - -
80A PHE 4.6 1.7 + - - -
82A ALA* 3.5 38.3 - - + +
83A LYS* 3.6 26.0 - - + +
90A PHE* 3.8 12.8 - + - -
93A ILE* 4.6 3.5 - - + +
263A PHE* 3.7 24.0 - + - -
175F ARG* 5.0 4.5 - - - -
235F ASP* 2.7 37.2 + - - -
237F PHE* 3.3 15.3 - + - -
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Residues in contact with ASP 77 (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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73A SER* 2.8 34.4 + - - +
74A THR* 4.6 0.2 - - - -
76A TYR* 1.3 92.8 - - - +
78A HIS* 1.3 81.3 + - + +
79A SER 3.7 0.2 - - - -
80A PHE* 4.7 3.6 + - - -
83A LYS* 4.3 19.6 + - - +
171F HIS* 4.5 11.3 + - - +
172F VAL 4.2 8.6 - - - +
173F THR* 3.7 4.7 - - - +
174F ARG* 2.7 36.0 + - - +
175F ARG* 5.4 1.2 + - - +
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Residues in contact with HIS 78 (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 ARG* 4.7 13.0 + - - +
59A PHE* 3.7 21.9 - + + -
74A THR* 2.9 43.3 + - + +
77A ASP* 1.3 86.2 + - + +
79A SER* 1.3 62.7 + - - +
80A PHE* 3.2 3.9 - - - +
42F GLY* 5.2 2.3 - - - -
43F VAL* 4.1 5.0 + - - +
170F GLN* 3.8 23.3 + - - +
171F HIS* 3.3 44.7 + - - +
172F VAL 4.1 5.8 - - - -
173F THR* 3.5 17.2 + - - +
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Residues in contact with SER 79 (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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55A LEU* 4.5 6.5 - - - -
59A PHE* 4.0 1.3 - - - -
75A MSE 2.7 24.0 + - - -
76A TYR 3.7 0.3 + - - -
77A ASP 3.7 0.2 - - - -
78A HIS* 1.3 77.6 - - - +
80A PHE* 1.3 65.9 + - - +
81A TRP* 3.0 10.4 + - - -
82A ALA* 3.1 24.3 + - - +
89A ILE* 4.0 16.1 - - - +
42F GLY* 3.4 0.7 - - - -
43F VAL* 2.8 47.4 + - - -
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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