Contacts of the helix formed by residues 155 - 166 (chain B) in PDB entry 5GGP
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 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A HIS* 6.3 2.9 - - + -
153B SER 3.4 1.4 + - - -
154B PRO* 1.3 86.6 - - + +
156B GLU* 1.3 63.2 + - - +
157B ASP* 3.1 14.5 + - - -
158B GLU* 2.7 49.8 + - - +
159B ALA* 3.5 4.9 + - - +
184B HIS* 4.6 0.6 - - - +
186B LYS* 5.0 1.8 - - - -
301B NA 3.2 17.5 - - - -
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 4.3 25.5 + - - +
148B VAL 4.5 2.6 - - - +
149B PHE* 3.9 10.9 - - - +
150B ASP* 3.0 57.6 + - + +
151B THR* 4.1 2.5 - - - +
153B SER* 3.7 10.0 + - - +
154B PRO 3.0 6.3 + - - +
155B HIS* 1.3 77.8 - - - +
157B ASP* 1.3 57.5 + - - +
159B ALA* 3.1 14.6 + - - +
160B MET* 2.9 27.4 + - - +
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Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B THR* 3.7 20.1 - - + +
155B HIS* 3.3 12.1 - - - -
156B GLU* 1.3 79.6 - - - +
158B GLU* 1.3 63.1 + - - +
160B MET* 3.3 5.3 + - - +
161B VAL* 3.0 32.4 + - - +
184B HIS 3.1 22.9 + - - +
185B LEU* 4.1 4.5 - - - -
186B LYS* 2.7 53.4 + - - +
189B ALA* 3.7 21.2 + - + +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B HIS* 2.7 43.7 + - - +
157B ASP* 1.3 80.6 + - - +
159B ALA* 1.3 64.0 + - - +
161B VAL* 3.2 8.1 + - - +
162B LEU* 3.0 34.8 + - + +
186B LYS* 2.9 24.3 + - - +
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ARG* 5.3 3.1 - - - +
149B PHE* 3.7 15.4 - - + -
155B HIS 3.5 3.7 + - - +
156B GLU* 3.1 21.6 + - - +
158B GLU* 1.3 77.8 - - - +
160B MET* 1.3 58.2 + - - +
162B LEU* 3.3 10.0 + - - +
163B PHE* 2.9 29.3 + - - +
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Residues in contact with MET 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE* 3.6 36.8 - - + -
133B VAL* 4.7 3.6 - - + -
149B PHE* 3.5 36.3 - - + -
151B THR* 4.4 4.9 - - + -
156B GLU 2.9 9.6 + - - +
157B ASP* 3.4 6.1 - - - +
158B GLU 3.2 0.2 - - - -
159B ALA* 1.3 77.6 - - - +
161B VAL* 1.3 57.4 + - + +
163B PHE* 3.3 2.4 + - - +
164B LEU* 2.9 45.6 + - + +
185B LEU* 3.8 29.6 - - + -
189B ALA* 4.0 20.4 - - + +
192B LEU* 6.3 0.9 - - + -
193B LEU* 4.7 13.7 - - + -
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ASP 3.0 19.7 + - - +
158B GLU* 3.2 10.3 + - - +
160B MET* 1.3 78.8 - - + +
162B LEU* 1.3 67.0 + - + +
164B LEU* 3.3 1.4 + - - +
165B ASN* 2.8 32.5 + - + +
188B THR* 4.8 14.8 - - + -
189B ALA* 3.6 31.2 - - + +
192B LEU* 4.1 24.7 - - + +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLU* 3.0 26.6 + - + +
159B ALA* 3.7 7.9 - - - +
161B VAL* 1.3 87.1 - - + +
163B PHE* 1.3 65.9 + - - +
165B ASN* 3.5 17.1 + - + +
166B MET* 3.6 13.2 + - - +
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Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLU 5.0 2.5 - - - -
133B VAL* 3.9 18.2 - - + -
135B VAL* 3.8 31.0 - - + -
145B ALA* 3.8 15.5 - - + -
147B ARG* 3.6 45.5 - - + +
149B PHE* 3.5 23.8 - + + -
159B ALA 2.9 14.3 + - - +
160B MET 3.4 6.7 - - - +
162B LEU* 1.3 76.9 - - - +
164B LEU* 1.3 74.3 + - + +
166B MET* 3.3 14.1 + - - +
167B VAL* 3.6 18.3 + - + +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 4.1 19.1 - - + -
160B MET* 2.9 37.8 + - + +
161B VAL 3.9 2.9 - - - +
163B PHE* 1.3 83.9 - - + +
165B ASN* 1.3 61.0 + - - +
167B VAL* 3.0 14.1 + - + +
173B LEU* 4.0 35.4 - - + -
175B CYS* 5.9 2.9 - - - -
192B LEU* 4.3 21.1 - - + -
193B LEU* 4.3 12.3 - - + -
196B LEU* 4.2 22.0 - - + -
216B LYS* 2.8 24.0 + - + +
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Residues in contact with ASN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B VAL* 2.8 22.0 + - + +
162B LEU* 3.6 11.0 + - + +
163B PHE 3.3 0.2 - - - -
164B LEU* 1.3 76.5 - - - +
166B MET* 1.3 79.8 + - - +
167B VAL 3.7 1.4 - - - +
192B LEU* 5.4 2.1 - - - +
216B LYS* 3.2 16.7 + - - +
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Residues in contact with MET 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LEU 3.6 8.5 + - - +
163B PHE* 3.3 8.9 + - - +
164B LEU 3.2 1.0 - - - -
165B ASN* 1.3 95.7 - - - +
167B VAL* 1.3 63.7 + - - +
168B ALA* 3.5 2.4 + - - +
303B NA 4.2 4.2 - - - -
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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