Contacts of the helix formed by residues 70 - 84 (chain E) in PDB entry 1U1C
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 GLY 70 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69E ILE* 1.3 77.3 - - - +
71E GLY* 1.3 61.3 + - - -
72E PRO* 3.5 3.4 - - - -
73E SER* 3.8 1.6 + - - -
74E THR* 2.7 31.6 + - - -
197E MET* 3.2 15.9 - - - -
198E GLU* 2.8 14.7 + - - -
72F PRO* 3.6 19.5 - - - -
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Residues in contact with GLY 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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70E GLY* 1.3 71.3 - - - -
72E PRO* 1.3 62.0 - - - +
74E THR* 3.2 3.4 + - - -
75E SER* 2.7 37.6 + - - -
117E ASP* 5.9 0.4 - - - +
119E ALA* 3.9 7.2 - - - -
160E ASP* 4.4 5.6 + - - -
197E MET 3.7 6.2 + - - -
198E GLU* 5.2 0.7 - - - -
201E THR* 3.2 29.9 - - - +
72F PRO* 4.2 2.4 - - - +
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Residues in contact with PRO 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ILE 5.3 0.4 - - - +
70E GLY* 3.5 4.7 - - - -
71E GLY* 1.3 89.1 - - - +
73E SER* 1.3 61.2 + - - +
75E SER* 2.7 19.4 + - - +
76E ILE* 3.3 12.8 + - - +
119E ALA* 4.6 2.9 - - + -
160E ASP* 4.7 1.8 - - - +
69F ILE 4.2 0.9 - - - +
70F GLY* 3.6 29.6 - - - +
72F PRO* 3.7 17.3 - - + -
160F ASP* 3.1 48.7 - - - +
197F MET* 3.9 14.3 - - + +
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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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49E GLU* 3.5 20.3 + - - -
50E PHE* 3.2 24.7 - - - -
67E THR 2.7 24.0 + - - +
69E ILE 3.7 7.8 + - - -
70E GLY 3.8 1.4 + - - -
71E GLY 3.5 0.2 - - - -
72E PRO* 1.3 76.8 - - - +
74E THR* 1.3 64.1 + - - +
76E ILE* 3.4 6.2 + - - +
77E ALA* 3.1 18.9 + - - +
1002E K 2.8 20.2 - - - -
69F ILE* 4.1 7.5 + - - -
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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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67E THR* 3.3 27.2 - - + -
68E GLY 4.1 0.2 + - - -
70E GLY 2.7 22.8 + - - -
71E GLY* 3.4 8.3 - - - -
73E SER* 1.3 78.3 + - - +
75E SER* 1.3 57.7 + - - +
77E ALA* 3.3 1.4 + - - +
78E VAL* 2.9 49.2 + - + +
91E ARG* 6.0 1.1 - - - -
198E GLU* 3.2 26.7 - - + +
201E THR* 4.6 1.6 - - + -
202E LEU* 4.2 25.6 - - + +
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Residues in contact with SER 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E GLY 2.7 17.7 + - - -
72E PRO* 2.7 21.7 + - - +
74E THR* 1.3 73.4 - - - +
76E ILE* 1.3 61.7 + - - +
79E GLU* 3.2 26.3 + - - +
119E ALA* 4.8 2.0 - - - -
123E PHE* 4.0 19.5 - - - -
201E THR* 4.0 6.5 - - - +
205E MET* 3.4 14.1 - - - +
161F THR* 3.0 28.9 + - - -
162F PHE 4.6 0.3 + - - -
163F TYR* 5.1 2.5 - - - -
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Residues in contact with ILE 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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8E HIS* 3.4 41.7 - - + +
9E LEU* 5.4 0.4 - - + -
50E PHE* 3.9 8.7 - - + -
72E PRO 3.3 10.9 + - - +
73E SER* 3.6 7.6 - - - +
74E THR 3.2 0.6 - - - -
75E SER* 1.3 77.4 + - - +
77E ALA* 1.3 66.7 + - - +
79E GLU* 3.4 1.2 + - - +
80E GLU* 3.0 33.1 + - - +
69F ILE* 3.9 39.9 - - + -
162F PHE* 3.7 33.2 - - + +
163F TYR* 4.7 6.7 - - + -
197F MET* 4.1 4.0 - - + -
5051F BAU 4.8 0.2 - - - -
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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
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9E LEU* 3.9 16.0 - - + +
24E VAL* 6.0 0.7 - - + -
50E PHE* 3.8 19.7 - - + -
65E CYS* 4.6 6.1 - - - -
66E SER 4.0 10.8 - - - +
67E THR* 4.4 11.4 - - + -
73E SER 3.1 16.2 + - - +
74E THR 3.8 2.7 - - - +
76E ILE* 1.3 77.8 - - - +
78E VAL* 1.3 57.8 + - - +
81E LEU* 3.0 39.2 + - + +
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Residues in contact with VAL 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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24E VAL* 5.6 3.4 - - + -
67E THR* 5.2 4.9 - - + -
74E THR* 2.9 30.9 + - + +
77E ALA* 1.3 75.5 - - + +
79E GLU* 1.3 60.0 + - - +
81E LEU* 3.4 0.7 + - - -
82E ALA* 2.9 28.4 + - - +
89E PHE* 3.5 36.7 - - + -
202E LEU* 3.8 22.4 - - + -
205E MET* 3.7 25.4 - - + -
206E CYS* 4.1 13.9 - - - -
211E LEU* 4.7 5.6 - - + -
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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 SER 3.2 20.0 + - - +
76E ILE 3.8 2.0 - - - +
77E ALA 3.4 0.2 - - - -
78E VAL* 1.3 78.6 - - - +
80E GLU* 1.3 58.7 + - - +
82E ALA* 3.3 5.4 + - - +
83E GLN* 2.7 48.5 + - - +
123E PHE* 5.4 5.3 - - + -
205E MET* 4.0 7.9 - - + +
209E GLN* 4.2 14.6 + - - +
163F TYR* 3.7 31.9 - - + -
171F THR* 3.4 14.3 - - - +
172F TYR* 2.9 33.9 + - - +
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Residues in contact with GLU 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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6E VAL* 3.5 17.3 - - + +
7E PHE* 3.6 5.6 - - - +
8E HIS* 2.6 55.8 + - - +
9E LEU* 3.0 30.0 + - + +
76E ILE* 3.0 22.2 + - - +
79E GLU* 1.3 73.9 - - - +
81E LEU* 1.3 62.8 + - - +
83E GLN* 3.5 8.3 + - - +
84E LEU* 3.2 28.1 + - - +
163F TYR* 2.7 28.2 + - + +
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Residues in contact with LEU 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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9E LEU* 3.8 16.8 - - + -
11E LEU* 4.4 12.8 - - + -
16E LEU* 5.2 2.9 - - + -
22E ALA* 4.2 6.7 - - + -
24E VAL* 4.2 12.6 - - + -
63E ILE* 4.0 21.8 - - + -
65E CYS* 3.9 26.5 - - + -
77E ALA* 3.0 28.2 + - + +
78E VAL 3.8 4.0 - - - +
80E GLU* 1.3 75.6 - - - +
82E ALA* 1.3 61.8 + - - +
84E LEU* 3.2 8.1 + - + +
85E GLY 3.1 6.4 + - - -
86E ILE* 2.9 40.4 + - + +
89E PHE* 3.8 20.0 - - + -
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Residues in contact with ALA 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 VAL 2.9 17.9 + - - +
79E GLU* 3.3 8.7 + - - +
81E LEU* 1.3 75.1 - - - +
83E GLN* 1.3 62.8 + - - +
85E GLY* 3.2 9.2 + - - -
86E ILE 3.5 18.1 + - - +
87E ARG* 3.7 10.0 + - - -
89E PHE* 4.2 1.3 - - + -
211E LEU* 4.3 15.0 - - + -
172F TYR* 3.7 39.4 - - + -
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Residues in contact with GLN 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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5E ASP 4.6 5.5 - - - +
6E VAL* 3.9 20.4 - - + +
13E LYS* 4.7 6.9 - - - +
79E GLU* 2.7 45.2 + - - +
80E GLU* 3.5 11.3 - - - +
81E LEU 3.2 0.2 - - - -
82E ALA* 1.3 75.4 - - - +
84E LEU* 1.3 61.3 + - + +
85E GLY* 3.3 1.1 + - - -
87E ARG* 5.7 0.3 + - - -
163F TYR* 4.3 14.2 + - - -
170F ASP 3.9 18.3 + - - +
171F THR* 4.1 2.2 - - - +
172F TYR* 4.3 14.3 - - + +
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Residues in contact with LEU 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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5E ASP* 3.9 15.0 - - + +
6E VAL* 4.0 15.0 - - + -
9E LEU* 4.5 0.9 - - + -
11E LEU* 3.7 46.2 - - + +
12E THR 3.6 4.3 - - - -
13E LYS* 3.4 53.5 - - + +
16E LEU* 3.5 31.5 - - + +
19E ALA 4.9 0.5 - - - +
80E GLU 3.2 18.6 + - - +
81E LEU* 3.2 10.3 + - + +
83E GLN* 1.3 76.1 - - - +
85E GLY* 1.3 55.7 + - - +
86E ILE 3.8 0.7 - - - -
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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