Contacts of the helix formed by residues 155 - 173 (chain B) in PDB entry 5GRH
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 LYS 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLY* 2.8 31.3 + - - +
154B THR* 1.3 70.5 - - - +
156B ALA* 1.3 66.5 + - - +
159B LEU* 3.1 43.5 + - + +
192B LEU* 3.7 18.7 - - + +
196B CYS* 3.7 19.1 - - - -
199B GLU* 4.5 17.2 + - - -
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY 4.8 0.2 + - - -
154B THR* 3.4 7.2 + - - +
155B LYS* 1.3 81.5 - - - +
157B LYS* 1.3 60.7 + - + +
159B LEU* 3.6 8.1 + - - +
160B ARG* 3.2 22.7 + - - +
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Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASP* 5.4 2.9 + - - -
129B GLU* 3.8 9.4 - - - +
131B THR* 3.3 29.6 + - - +
132B GLU* 3.3 37.4 + - - +
136B SER* 5.4 1.2 + - - -
154B THR* 3.2 16.6 + - - +
156B ALA* 1.3 77.2 - - + +
158B SER* 1.3 64.0 + - - +
159B LEU 3.3 0.4 - - - -
160B ARG* 3.1 40.0 - - - +
161B ILE* 3.4 13.7 + - - +
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU* 5.3 1.0 - - - +
132B GLU* 3.9 2.1 + - - -
153B ILE* 3.7 16.1 - - - +
154B THR 2.8 22.3 + - - -
155B LYS 3.3 0.2 + - - -
157B LYS* 1.3 76.9 - - - +
159B LEU* 1.3 62.4 + - - +
161B ILE* 3.3 22.0 - - - +
162B ALA* 3.3 13.2 + - - +
192B LEU* 5.2 0.6 - - - +
193B PHE* 3.6 28.8 + - - -
196B CYS* 3.8 26.2 - - - +
197B CYS* 5.0 0.2 - - - -
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Residues in contact with LEU 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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155B LYS* 3.1 43.1 + - + +
156B ALA* 3.9 7.9 - - - +
157B LYS 3.3 0.4 - - - -
158B SER* 1.3 76.3 - - - +
160B ARG* 1.3 54.7 + - - +
162B ALA* 3.2 3.1 + - - +
163B GLU* 2.6 40.3 + - - +
196B CYS* 3.3 37.5 - - + +
199B GLU* 4.0 18.8 - - + +
200B VAL* 4.0 12.6 - - + +
203B ARG* 5.0 5.2 - - - +
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Residues in contact with ARG 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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101B ASP* 2.8 35.8 + - - -
103B TYR* 3.2 63.3 + - + +
129B GLU* 4.3 1.3 - - - -
131B THR* 3.7 12.3 + - - -
156B ALA 3.2 15.0 + - - +
157B LYS* 3.1 38.2 - - - +
159B LEU* 1.3 79.8 - - - +
161B ILE* 1.3 54.7 + - - +
163B GLU* 3.6 7.9 - - - +
164B TYR* 2.8 29.8 + - - +
262B HIS* 3.8 19.3 + - + +
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Residues in contact with ILE 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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103B TYR* 3.6 19.3 - - + +
104B ALA* 3.9 11.2 - - + -
127B VAL* 3.6 19.8 - - + +
128B ARG 3.5 24.9 - - - +
129B GLU* 3.6 24.5 - - + +
157B LYS 3.5 13.5 - - - +
158B SER* 3.3 15.0 - - - +
160B ARG* 1.3 80.9 - - - +
162B ALA* 1.3 60.9 + - - +
164B TYR* 3.6 2.5 + - + +
165B ALA* 3.1 25.8 + - - +
193B PHE* 3.8 23.6 - - + -
232B VAL* 3.8 13.5 - - + +
233B MET 4.6 0.4 - - - +
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Residues in contact with ALA 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 SER 3.3 15.7 - - - +
159B LEU 3.2 4.2 + - - +
161B ILE* 1.3 80.0 - - - +
163B GLU* 1.3 64.5 + - - +
165B ALA* 3.5 1.2 + - - +
166B PHE* 3.2 34.0 + - + -
196B CYS 4.1 0.7 - - - +
197B CYS* 3.8 31.0 - - - -
200B VAL* 3.8 17.3 - - + -
232B VAL* 4.4 8.3 - - - -
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 2.6 23.5 + - - +
160B ARG* 3.6 10.3 - - - +
162B ALA* 1.3 74.5 - - - +
164B TYR* 1.3 59.8 + - - +
166B PHE* 4.2 0.9 - - - +
167B LYS* 3.2 25.6 + - + +
200B VAL* 3.5 26.5 - - - +
203B ARG* 3.5 29.7 + - - -
204B TYR* 3.8 19.4 + - - +
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Residues in contact with TYR 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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103B TYR* 4.0 24.0 - + + +
104B ALA* 3.8 15.7 - - + -
106B VAL* 3.7 22.2 - - + -
127B VAL* 4.2 9.6 - - + -
160B ARG 2.8 16.6 + - - +
161B ILE* 3.7 6.7 - - + +
162B ALA 3.2 0.2 - - - -
163B GLU* 1.3 74.9 - - - +
165B ALA* 1.3 60.6 + - - +
167B LYS* 3.2 11.2 + - + +
168B LEU* 2.8 51.4 + - + +
260B TYR* 3.0 48.1 - + + -
261B GLY 5.8 1.6 - - - -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 4.2 22.0 - - + +
161B ILE 3.1 15.2 + - - +
162B ALA 3.8 5.2 - - - +
163B GLU 3.5 0.2 - - - -
164B TYR* 1.3 78.2 - - - +
166B PHE* 1.3 51.5 + - + +
168B LEU* 3.2 4.4 + - - +
169B ALA* 2.6 37.0 + - - +
177B VAL* 4.5 9.6 - - + +
230B VAL* 4.6 5.6 - - + +
232B VAL* 3.8 29.4 - - + -
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Residues in contact with PHE 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 ALA* 3.2 28.6 + - + +
163B GLU 4.2 0.4 - - - +
165B ALA* 1.3 78.6 - - + +
167B LYS* 1.3 58.0 + - - +
169B ALA* 3.4 6.4 - - - +
170B GLN* 2.8 31.4 + - - +
177B VAL* 4.1 20.2 - - + -
197B CYS* 3.9 17.9 - - + -
200B VAL* 3.6 8.7 - - + -
201B ALA* 3.7 24.0 - - + -
204B TYR* 3.5 45.3 - + + -
207B ILE* 3.9 30.4 - - + +
209B PHE* 3.6 32.3 - + + -
232B VAL* 5.6 1.1 - - + -
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Residues in contact with LYS 167 (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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163B GLU* 3.2 20.6 + - + +
164B TYR* 3.6 11.0 - - + +
166B PHE* 1.3 77.3 - - - +
168B LEU* 1.3 58.8 + - - +
170B GLN* 3.5 0.8 + - - +
171B GLU* 2.5 68.1 + - + +
204B TYR* 3.6 19.9 + - + +
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Residues in contact with LEU 168 (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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106B VAL* 3.9 24.2 - - + -
125B LEU* 3.8 23.8 - - + -
127B VAL* 4.1 17.7 - - + -
164B TYR* 2.8 36.3 + - + +
165B ALA 3.5 3.4 - - - +
167B LYS* 1.3 74.2 - - - +
169B ALA* 1.3 65.9 + - - +
171B GLU* 4.8 6.3 - - + +
172B SER* 2.8 44.9 + - - +
230B VAL* 5.5 1.1 - - + -
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Residues in contact with ALA 169 (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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165B ALA 2.6 21.6 + - - +
166B PHE* 3.4 5.6 - - - +
168B LEU* 1.3 75.2 - - - +
170B GLN* 1.3 60.4 + - - +
172B SER* 3.5 0.8 + - - -
173B GLY 3.3 3.5 + - - -
174B ARG* 3.0 35.8 + - + +
176B LYS 5.4 0.2 - - - +
177B VAL* 3.6 26.9 - - + -
207B ILE* 4.4 10.5 - - + -
230B VAL* 4.1 19.5 - - + +
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Residues in contact with GLN 170 (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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166B PHE 2.8 20.0 + - - +
167B LYS* 3.9 4.3 - - - +
169B ALA* 1.3 72.7 - - - +
171B GLU* 1.3 66.7 + - + +
173B GLY* 3.2 13.7 + - - -
174B ARG 5.0 0.4 - - - -
204B TYR* 3.7 29.0 - - + +
205B PRO* 6.0 0.3 - - - +
206B GLN* 3.1 40.8 + - - +
207B ILE* 4.0 14.8 - - + +
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Residues in contact with GLU 171 (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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167B LYS* 2.5 56.5 + - + +
168B LEU* 4.3 6.4 - - + +
170B GLN* 1.3 82.1 - - + +
172B SER* 1.3 60.7 + - - +
173B GLY 3.4 0.3 + - - -
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Residues in contact with SER 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.2 5.0 - - - +
168B LEU* 2.8 39.3 + - - +
169B ALA 4.0 3.1 - - - -
171B GLU* 1.3 75.8 - - - +
173B GLY* 1.3 62.5 + - - +
174B ARG* 4.0 24.0 - - - +
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Residues in contact with GLY 173 (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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169B ALA 3.3 0.2 + - - -
170B GLN 3.2 11.9 + - - -
171B GLU 3.2 4.6 - - - -
172B SER* 1.3 80.0 - - - +
174B ARG* 1.3 63.6 + - - +
175B LYS* 5.7 1.4 - - - +
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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
------------------------------------------------------------
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