Contacts of the helix formed by residues 123 - 136 (chain E) in PDB entry 5Y3A
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 123 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D PHE* 3.5 26.6 - + + -
54D ARG 2.9 29.4 + - - -
55D LEU* 3.1 22.7 + - - -
104E LEU* 3.9 2.7 - - + -
118E THR 3.7 17.2 + - - -
119E LEU* 3.9 5.0 - - + +
120E SER* 3.1 29.2 + - - +
122E GLU* 1.3 100.2 + - - +
124E ALA* 1.3 65.5 + - - +
125E GLY 3.3 3.0 + - - -
126E VAL* 3.4 9.2 + - - +
127E ILE* 3.1 41.7 + - + +
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Residues in contact with ALA 124 (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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101C GLY* 5.3 0.7 - - - -
104E LEU* 4.2 8.9 - - + +
106E THR* 3.3 30.4 - - + +
110E GLY 3.4 15.7 - - - +
112E ASN* 4.3 11.7 - - + +
120E SER 3.9 2.3 + - - +
121E ASP 3.2 19.0 + - - +
123E HIS* 1.3 78.3 - - - +
125E GLY* 1.3 56.6 + - - +
127E ILE* 3.8 1.0 - - - +
128E SER* 2.9 31.6 + - - -
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Residues in contact with GLY 125 (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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99C ASN* 3.4 19.1 - - - -
101C GLY* 3.6 8.7 - - - -
102C LEU* 3.6 21.5 - - - -
105C SER* 5.2 1.5 - - - -
110E GLY 3.9 1.8 + - - -
121E ASP 4.9 0.4 + - - -
122E GLU 5.4 0.8 - - - -
123E HIS 3.3 0.6 - - - -
124E ALA* 1.3 74.9 - - - +
126E VAL* 1.3 63.1 + - - +
128E SER* 3.0 13.7 + - - -
129E VAL* 3.1 19.2 + - - +
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Residues in contact with VAL 126 (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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102C LEU* 4.2 20.9 - - + -
105C SER* 4.5 12.5 + - - +
49D THR* 3.8 25.0 - - + +
52D GLY* 4.1 18.8 - - - +
53D PHE* 3.8 27.8 - - + -
122E GLU 5.8 1.3 - - - +
123E HIS* 3.4 10.8 + - - +
125E GLY* 1.3 74.1 - - - +
127E ILE* 1.3 63.8 + - - +
129E VAL* 4.0 1.2 - - - +
130E LEU* 3.1 39.0 + - + +
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Residues in contact with ILE 127 (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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53D PHE* 4.5 18.6 - - + -
104E LEU* 3.9 25.4 - - + -
106E THR* 4.8 1.6 - - - +
119E LEU* 4.7 5.4 - - + -
123E HIS* 3.1 37.8 + - + +
124E ALA 3.8 4.3 - - - +
126E VAL* 1.3 76.7 - - - +
128E SER* 1.3 61.4 + - - +
130E LEU* 3.7 7.8 + - + +
131E ALA* 3.5 8.5 + - - +
156E ILE* 5.2 0.9 - - + -
158E ILE* 3.4 38.1 - - + +
165E THR* 4.2 10.3 - - + +
166E VAL 4.8 0.2 - - - -
167E ALA* 3.7 36.1 - - + +
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Residues in contact with SER 128 (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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99C ASN* 2.9 26.7 + - - -
106E THR* 3.9 14.1 - - - -
107E ASP 4.1 8.1 - - - -
110E GLY* 3.3 10.3 - - - -
124E ALA 2.9 19.2 + - - -
125E GLY 3.0 6.4 + - - -
127E ILE* 1.3 73.4 - - - +
129E VAL* 1.3 62.1 + - - +
131E ALA* 3.4 5.4 + - - +
132E GLN* 3.2 31.4 + - - +
165E THR* 4.2 13.6 + - - +
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Residues in contact with VAL 129 (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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99C ASN* 3.5 32.5 - - + +
102C LEU* 3.6 23.3 - - + -
49D THR* 3.8 15.3 - - + +
125E GLY 3.1 18.7 + - - +
126E VAL 4.0 2.2 - - - +
127E ILE 3.5 0.2 - - - -
128E SER* 1.3 72.3 + - - +
130E LEU* 1.3 60.4 + - - +
132E GLN* 3.1 11.2 + - - +
133E GLN* 2.9 56.1 + - + +
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Residues in contact with LEU 130 (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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46D LEU* 3.2 53.1 - - + +
49D THR* 3.9 5.8 - - + -
50D ALA* 3.7 21.8 - - + +
53D PHE* 5.8 0.7 - - + -
126E VAL* 3.1 38.4 + - + +
127E ILE* 3.7 9.4 - - + +
129E VAL* 1.3 76.9 - - - +
131E ALA* 1.3 56.3 + - - +
133E GLN* 3.4 0.4 + - - -
134E ALA* 2.9 32.6 + - - +
147E VAL* 4.0 16.8 - - + +
149E LEU* 4.2 24.7 - - + -
158E ILE* 4.6 7.2 - - + -
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Residues in contact with ALA 131 (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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127E ILE 3.5 1.8 + - - +
128E SER 3.4 9.5 + - - +
129E VAL 3.3 0.4 - - - -
130E LEU* 1.3 77.2 - - - +
132E GLN* 1.3 60.9 + - - +
134E ALA* 4.2 1.2 - - - +
135E ALA* 3.5 20.4 + - - +
145E PRO* 4.7 5.1 - - - +
147E VAL* 4.3 11.6 - - + +
158E ILE* 3.9 22.6 - - + +
159E GLN* 5.2 0.7 - - - -
160E LYS* 3.7 35.9 - - + +
165E THR* 3.9 4.9 - - + -
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Residues in contact with GLN 132 (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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99C ASN* 4.0 12.9 - - - +
108E SER* 3.4 32.5 + - - +
128E SER* 3.2 20.5 + - - +
129E VAL* 3.1 14.8 + - + +
131E ALA* 1.3 76.4 - - - +
133E GLN* 1.3 63.6 + - + +
135E ALA* 3.6 12.0 - - - +
136E LYS* 3.4 18.3 - - - +
160E LYS* 3.8 29.2 - - - +
165E THR* 4.9 1.2 + - - -
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Residues in contact with GLN 133 (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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15C SER 5.5 3.0 + - - -
17C GLU* 5.8 4.4 - - - +
42D ALA* 5.6 4.8 - - - +
45D GLU* 3.3 37.3 + - - +
46D LEU* 2.7 46.1 - - + +
49D THR* 3.3 24.9 + - - -
129E VAL* 2.9 30.7 + - + +
132E GLN* 1.3 75.6 - - + +
134E ALA* 1.3 60.9 + - - +
136E LYS* 3.1 29.9 + - - +
137E LEU* 4.0 6.2 - - - +
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Residues in contact with ALA 134 (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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46D LEU* 4.4 7.1 - - + +
68D VAL* 3.8 16.4 - - + -
70D PHE* 3.4 13.0 - - - -
130E LEU 2.9 18.0 + - - +
131E ALA 4.2 1.8 - - - +
132E GLN 3.4 0.2 - - - -
133E GLN* 1.3 74.4 - - - +
135E ALA* 1.3 64.1 + - - +
136E LYS 3.2 0.2 - - - -
137E LEU* 3.3 28.7 + - + +
145E PRO* 3.9 8.5 - - + -
147E VAL* 3.6 24.0 - - + -
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Residues in contact with ALA 135 (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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131E ALA 3.5 12.5 + - - +
132E GLN* 3.6 13.2 - - - +
134E ALA* 1.3 76.9 - - - +
136E LYS* 1.3 59.3 + - + +
137E LEU 3.1 7.2 + - - -
138E THR* 3.5 24.6 + - - +
140E ASP 5.1 1.0 - - - +
143E ASP 5.6 0.2 - - - -
144E ILE* 5.9 4.7 - - + -
145E PRO* 3.9 16.7 - - + +
160E LYS* 6.4 1.1 - - + -
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Residues in contact with LYS 136 (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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17C GLU* 5.1 10.3 + - - -
38D GLN* 5.5 2.8 - - - +
42D ALA* 4.6 9.1 - - + +
132E GLN 3.4 18.4 - - - +
133E GLN* 3.1 16.9 + - - +
135E ALA* 1.3 75.5 - - + +
137E LEU* 1.3 61.3 + - - +
138E THR 3.7 3.8 - - - -
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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