Contacts of the helix formed by residues 151 - 169 (chain E) in PDB entry 3F7G
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 CYS 151 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124E CYS* 4.0 1.3 - - - -
126E PHE* 4.2 4.0 - - - -
127E CYS* 3.7 19.5 - - + -
144E HIS* 3.4 6.5 - - - +
148E PHE* 3.1 16.7 + - - +
149E PRO 3.3 0.6 - - - -
150E SER* 1.3 76.5 + - - +
152E GLN* 1.3 63.2 + - - +
153E PHE* 3.6 12.6 - - - -
154E LEU* 3.4 19.7 + - + +
155E LEU* 2.9 30.0 + - - +
1001E ZN 2.3 37.2 - - - -
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Residues in contact with GLN 152 (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 GLY 5.7 2.4 + - - -
126E PHE* 3.5 30.9 - - + -
150E SER 4.1 9.6 - - - +
151E CYS* 1.3 70.6 - - - +
153E PHE* 1.3 60.1 + - - +
155E LEU* 3.9 12.0 - - + +
156E ARG* 2.8 43.5 + - + +
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Residues in contact with PHE 153 (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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160D ARG* 5.0 15.0 - - - -
90E ARG* 4.0 15.0 - - - -
110E ALA 3.8 11.9 - - - -
111E ALA 4.1 2.9 - - - -
112E GLY* 3.4 26.2 - - - -
124E CYS* 4.7 1.1 - - - -
125E PHE* 3.6 26.7 - + - -
126E PHE* 3.5 31.6 - + + -
141E TRP* 3.6 19.3 - + - -
144E HIS* 4.5 5.4 - + - -
151E CYS* 3.3 3.7 - - - -
152E GLN* 1.3 78.3 - - - +
154E LEU* 1.3 57.2 + - - +
156E ARG* 3.4 4.7 + - - +
157E SER* 2.7 50.5 + - - -
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Residues in contact with LEU 154 (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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141E TRP* 3.6 43.5 - - + +
144E HIS* 3.7 12.3 - - + +
145E ALA* 3.5 28.5 - - + +
148E PHE 3.5 23.6 - - - +
149E PRO* 4.1 7.4 - - + +
151E CYS* 3.4 16.7 + - + +
152E GLN 3.4 0.2 - - - -
153E PHE* 1.3 79.2 - - - +
155E LEU* 1.3 56.8 + - - +
158E LYS* 2.8 43.2 + - + +
162E PHE* 4.5 0.4 - - + -
163E VAL* 3.7 22.6 - - + +
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Residues in contact with LEU 155 (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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155D LEU 4.8 1.0 - - - +
156D ARG* 4.5 3.6 - - - +
159D GLY* 4.7 0.2 - - - -
149E PRO 3.9 17.0 - - - +
150E SER* 4.1 13.2 - - - +
151E CYS 2.9 24.4 + - - +
152E GLN* 3.9 11.0 - - + +
153E PHE 3.3 0.2 - - - -
154E LEU* 1.3 73.4 - - - +
156E ARG* 1.3 57.6 + - + +
159E GLY* 2.8 31.9 + - - +
160E ARG* 4.1 29.7 + - + +
163E VAL* 3.8 28.3 - - + -
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Residues in contact with ARG 156 (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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155D LEU* 4.3 4.7 - - - +
156D ARG* 6.4 0.7 - - - +
159D GLY* 3.6 3.3 - - - -
160D ARG* 3.1 48.5 + - - +
126E PHE* 6.5 1.3 - - - -
152E GLN* 2.8 31.7 + - + +
153E PHE* 3.9 4.3 - - - +
155E LEU* 1.3 74.1 - - + +
157E SER* 1.3 59.5 + - - +
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Residues in contact with SER 157 (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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158D LYS 4.8 0.2 - - - +
159D GLY 3.5 1.0 - - - -
160D ARG* 3.0 32.0 + - - +
161D ASP* 3.1 27.8 + - - +
141E TRP* 3.3 31.9 - - - -
153E PHE* 2.7 40.1 + - - -
156E ARG* 1.3 77.9 - - - +
158E LYS* 1.3 59.3 + - - +
159E GLY 3.7 0.2 - - - -
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Residues in contact with LYS 158 (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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158D LYS* 3.1 13.4 - - - +
159D GLY* 3.6 4.9 - - - -
161D ASP* 4.2 12.2 + - + +
139E ASP* 5.8 0.4 + - - -
141E TRP* 3.5 56.6 - - + +
154E LEU* 2.8 23.9 + - + +
157E SER* 1.3 76.9 - - - +
159E GLY* 1.3 62.1 + - - +
162E PHE* 3.4 60.7 + - + +
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Residues in contact with GLY 159 (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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156D ARG 3.4 10.3 - - - -
157D SER 3.4 7.9 - - - -
159D GLY* 3.4 12.0 - - - -
155E LEU* 2.8 27.8 + - - -
158E LYS* 1.3 77.7 - - - +
160E ARG* 1.3 64.9 + - - -
161E ASP 3.3 3.5 + - - -
162E PHE 3.5 0.2 + - - -
163E VAL* 3.5 20.8 + - - +
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Residues in contact with ARG 160 (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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153D PHE* 5.8 3.4 - - - -
156D ARG* 2.9 60.9 + - + +
157D SER* 3.3 12.7 + - - +
155E LEU* 4.1 24.1 + - + -
159E GLY* 1.3 69.3 - - - -
161E ASP* 1.3 67.4 + - - +
163E VAL* 3.3 2.6 + - - +
164E HIS* 2.9 33.5 + - + +
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Residues in contact with ASP 161 (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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141D TRP* 4.6 5.0 + - - -
157D SER* 3.2 24.5 + - - +
158D LYS* 2.7 34.9 + - - +
160E ARG* 1.3 82.2 + - - +
162E PHE* 1.3 57.1 - - - +
164E HIS* 3.4 6.1 + - - +
165E SER* 2.9 30.5 + - - -
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Residues in contact with PHE 162 (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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139E ASP* 4.6 2.5 - - - -
141E TRP* 3.8 20.6 - - + -
142E THR* 3.8 27.1 - - - -
145E ALA* 3.8 13.2 - - + -
154E LEU* 4.5 0.7 - - + -
158E LYS* 3.4 65.4 + - + +
159E GLY 3.5 2.3 + - - +
160E ARG 3.3 0.4 - - - -
161E ASP* 1.3 78.7 - - - +
163E VAL* 1.3 69.5 + - + +
165E SER* 3.2 7.0 + - - -
166E VAL* 3.0 36.5 + - + +
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Residues in contact with VAL 163 (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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145E ALA* 4.2 9.2 - - + -
149E PRO* 3.5 40.6 - - + +
154E LEU* 3.7 34.5 - - + +
155E LEU* 3.8 18.8 - - + -
159E GLY 3.5 13.7 + - - +
160E ARG 3.3 6.7 + - - +
162E PHE* 1.3 81.7 - - + +
164E HIS* 1.3 58.3 + - - +
166E VAL* 3.3 3.3 + - - +
167E GLN* 2.9 31.3 + - + +
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Residues in contact with HIS 164 (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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160E ARG* 2.9 18.2 + - + +
161E ASP* 3.6 7.1 + - - +
163E VAL* 1.3 79.3 - - - +
165E SER* 1.3 58.0 + - - +
167E GLN* 3.8 6.6 - - + +
168E GLU* 2.9 54.0 + - + +
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Residues in contact with SER 165 (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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161E ASP 2.9 18.6 + - - -
162E PHE* 3.5 8.3 - - - -
164E HIS* 1.3 75.6 + - - +
166E VAL* 1.3 67.9 + - - +
168E GLU* 3.3 25.5 + - - +
169E THR* 3.4 15.4 + - - +
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Residues in contact with VAL 166 (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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142E THR* 3.7 18.4 - - + +
145E ALA* 3.8 4.7 - - + -
146E LYS* 3.6 45.5 - - + +
162E PHE* 3.0 48.1 + - + +
163E VAL 3.7 6.3 - - - +
165E SER* 1.3 76.2 - - - +
167E GLN* 1.3 63.7 + - - +
169E THR* 3.2 24.1 + - - +
170E HIS 4.0 5.5 - - - +
171E SER 4.8 0.2 + - - -
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Residues in contact with GLN 167 (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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145E ALA 3.0 11.9 - - - +
146E LYS 2.9 26.2 - - - +
149E PRO* 3.5 30.8 - - + +
163E VAL* 2.9 19.8 + - + +
164E HIS* 3.9 7.9 - - + +
165E SER 3.3 0.2 - - - -
166E VAL* 1.3 76.9 - - - +
168E GLU* 1.3 62.7 + - - +
170E HIS* 3.3 14.0 + - - -
171E SER* 3.5 14.6 + - - -
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Residues in contact with GLU 168 (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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164E HIS* 2.9 39.6 + - + +
165E SER* 3.4 14.8 + - - +
167E GLN* 1.3 77.0 - - - +
169E THR* 1.3 62.1 + - + +
170E HIS* 2.9 16.3 + - - -
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Residues in contact with THR 169 (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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165E SER* 3.4 15.1 + - - +
166E VAL* 3.2 15.4 + - - +
168E GLU* 1.3 77.4 - - + +
170E HIS* 1.3 74.4 + - - +
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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