Contacts of the helix formed by residues 112 - 126 (chain E) in PDB entry 3O2Q
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 GLU 112 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E SER* 5.4 2.8 + - - -
18E ARG* 2.7 34.6 + - - +
110E THR* 3.9 0.2 + - - -
111E CYS* 1.3 77.5 - - - +
113E GLU* 1.3 66.6 + - - +
114E ARG* 3.9 20.4 + - - +
115E VAL* 3.1 25.4 + - + +
116E TYR 3.0 15.2 + - - -
138E ASN* 2.9 15.3 + - - +
140E ASP* 3.2 15.3 - - - +
141E ILE 4.7 2.2 - - - +
143E ASP* 4.7 2.4 - - - +
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Residues in contact with GLU 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D LYS* 2.8 35.9 + - - +
112E GLU* 1.3 74.3 - - - +
114E ARG* 1.3 62.8 + - - +
116E TYR* 3.3 4.2 + - + +
117E ASP* 3.0 25.8 + - - +
138E ASN* 4.1 7.6 - - - +
140E ASP* 3.0 20.4 + - - +
188E LEU* 4.0 21.1 - - + +
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Residues in contact with ARG 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E SER* 5.9 5.3 - - - -
39E GLY* 5.9 4.2 - - - -
112E GLU* 3.4 18.0 + - - +
113E GLU* 1.3 75.9 - - - +
115E VAL* 1.3 57.7 + - + +
117E ASP* 3.4 12.6 + - + +
118E GLN* 3.0 59.9 + - + +
3F PRO* 4.9 17.6 - - - +
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Residues in contact with VAL 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E VAL* 3.5 47.8 - - + +
12E SER* 3.6 23.6 - - - +
13E SER* 3.8 12.6 - - - +
38E THR* 3.7 9.9 - - - +
110E THR* 3.9 5.6 - - + -
112E GLU* 3.1 31.1 + - + +
114E ARG* 1.3 75.2 - - + +
116E TYR* 1.3 65.8 + - - +
118E GLN* 3.0 9.0 + - - +
119E VAL* 2.9 23.7 + - - +
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Residues in contact with TYR 116 (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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296D SER* 4.1 7.4 + - - -
299D LYS* 3.6 27.8 - - + -
300D ASN* 5.1 2.8 + - - -
110E THR* 3.4 22.9 - - - +
112E GLU 3.0 9.2 + - - +
113E GLU* 3.4 8.5 - - - +
115E VAL* 1.3 75.5 - - - +
117E ASP* 1.3 68.8 + - - +
119E VAL* 3.1 2.9 + - - +
120E VAL* 2.8 43.0 + - + +
136E VAL* 4.0 28.9 - - + -
138E ASN* 3.5 21.3 - - + +
188E LEU* 3.7 26.2 - - + +
189E HIS 3.6 8.0 + - - -
190E THR* 3.2 37.6 + - + +
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Residues in contact with ASP 117 (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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299D LYS* 3.0 36.6 + - - -
113E GLU* 3.0 23.3 + - - +
114E ARG* 3.5 13.9 - - + +
116E TYR* 1.3 78.9 - - - +
118E GLN* 1.3 64.3 + - + +
120E VAL* 4.1 4.6 - - - +
121E GLU* 3.0 27.7 + - - +
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Residues in contact with GLN 118 (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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13E SER* 5.2 2.6 - - - -
38E THR* 2.7 52.1 + - - +
39E GLY* 4.6 3.3 + - - -
99E GLN* 4.7 6.1 + - - +
114E ARG* 3.0 58.3 + - + +
115E VAL* 3.0 9.7 + - - +
117E ASP* 1.3 78.4 - - + +
119E VAL* 1.3 58.3 + - - +
121E GLU* 3.9 4.1 - - - +
122E ASP* 3.0 30.0 + - - +
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Residues in contact with VAL 119 (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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11E VAL* 4.0 16.6 - - + -
38E THR* 3.9 17.7 - - + -
98E PHE* 3.9 29.1 - - + -
108E ILE* 4.2 6.3 - - + -
110E THR* 3.9 16.8 - - + -
115E VAL 2.9 15.7 + - - +
116E TYR 3.5 6.3 - - - +
118E GLN* 1.3 74.7 - - - +
120E VAL* 1.3 66.6 + - - +
122E ASP* 3.2 2.4 + - - +
123E LEU* 3.0 35.0 + - + +
136E VAL* 4.1 22.7 - - + -
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Residues in contact with VAL 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D ASN* 3.9 23.8 - - - +
303D LEU* 4.2 16.4 - - + -
116E TYR* 2.8 40.9 + - + +
117E ASP* 4.2 4.5 - - - +
119E VAL* 1.3 72.4 - - - +
121E GLU* 1.3 58.0 + - - +
123E LEU* 4.0 0.9 - - - +
124E ASN* 2.9 35.5 + - + +
136E VAL* 4.6 6.7 - - + -
190E THR* 3.6 28.0 - - + +
192E CYS* 4.2 18.5 - - - -
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Residues in contact with GLU 121 (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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303D LEU* 4.0 25.3 - - + +
117E ASP 3.0 20.0 + - - +
118E GLN* 3.9 4.9 - - - +
120E VAL* 1.3 74.4 - - - +
122E ASP* 1.3 69.0 + - - +
124E ASN* 4.0 5.8 + - - +
125E SER* 3.3 23.9 + - - -
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Residues in contact with ASP 122 (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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98E PHE* 3.4 19.6 - - + -
99E GLN* 3.6 30.8 - - + +
118E GLN 3.0 18.7 + - - +
119E VAL* 3.2 3.5 + - - +
121E GLU* 1.3 78.9 + - - +
123E LEU* 1.3 59.5 + - - +
125E SER* 3.0 24.2 + - - -
126E ARG* 3.0 43.0 + - - +
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Residues in contact with LEU 123 (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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98E PHE* 3.8 22.4 - - + -
108E ILE* 4.0 26.0 - - + -
119E VAL* 3.0 23.5 + - + +
122E ASP* 1.3 70.3 - - - +
124E ASN* 1.3 62.9 + - - +
125E SER 3.0 6.1 + - - -
126E ARG* 3.2 50.1 + - - +
128E GLN* 5.8 0.3 - - - +
134E VAL* 4.2 8.7 - - + -
136E VAL* 4.8 1.3 - - + -
192E CYS* 3.9 33.0 - - + -
193E PHE 4.6 12.2 - - - +
194E TYR* 4.6 16.8 - - + -
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Residues in contact with ASN 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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262D ASN* 5.2 3.6 - - - +
265D ARG* 5.3 11.5 + - - +
303D LEU* 3.5 33.0 - - + +
304D HIS* 3.4 22.9 + - - -
307D SER* 5.3 10.1 - - - -
120E VAL* 2.9 23.7 + - + +
121E GLU* 4.3 4.6 + - - +
123E LEU* 1.3 77.0 - - - +
125E SER* 1.3 58.9 + - - +
126E ARG 4.2 3.4 - - - +
128E GLN* 5.4 7.4 - - - +
192E CYS* 5.4 4.3 - - - -
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Residues in contact with SER 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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121E GLU* 3.3 17.5 + - - -
122E ASP* 3.0 19.5 + - - -
123E LEU 3.0 0.8 - - - -
124E ASN* 1.3 80.3 - - - +
126E ARG* 1.3 63.1 + - - +
127E GLU* 3.7 3.6 + - - +
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Residues in contact with ARG 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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98E PHE* 3.5 18.6 + - - -
99E GLN* 4.0 8.2 + - - +
101E CYS 2.9 28.6 + - - -
102E LYS* 3.8 31.0 - - - +
103E ASP 5.7 1.4 + - - -
122E ASP* 3.0 42.8 + - - +
123E LEU* 3.2 37.1 + - - +
124E ASN 4.2 3.8 - - - +
125E SER* 1.3 79.4 - - - +
127E GLU* 1.3 67.8 + - - +
128E GLN* 3.4 8.3 + - - +
193E PHE 5.1 1.8 - - - +
194E TYR* 6.0 3.5 - - - -
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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