Contacts of the helix formed by residues 161 - 180 (chain g) in PDB entry 5GJQ
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 SER 161 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16g PHE* 3.9 2.5 - - - -
17g GLU* 4.9 4.3 - - - +
159g VAL 4.3 0.2 + - - -
160g LEU* 1.3 74.7 - - - +
162g GLN* 1.3 64.0 + - - +
163g THR* 2.9 23.6 + - - -
164g GLU* 3.0 25.7 + - - +
165g ALA* 3.0 22.7 + - - +
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Residues in contact with GLN 162 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16g PHE* 3.6 41.3 - - + -
21g VAL* 5.6 0.7 - - + +
161g SER* 1.3 75.1 - - - +
163g THR* 1.3 61.4 + - + +
165g ALA* 3.5 2.1 + - - +
166g ARG* 2.9 34.3 + - + +
191g THR* 3.7 23.2 + - + +
193g THR* 3.9 16.9 - - - +
198g GLU* 4.8 9.7 + - - -
200g GLU* 5.4 3.2 + - - -
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Residues in contact with THR 163 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161g SER* 2.9 21.6 + - - -
162g GLN* 1.3 78.9 - - + +
164g GLU* 1.3 62.6 + - - +
166g ARG* 3.2 7.1 + - - +
167g ASP* 2.9 30.5 + - - +
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Residues in contact with GLU 164 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157g GLN* 3.0 35.6 + - - +
159g VAL 4.1 0.3 - - - +
160g LEU* 3.5 14.6 - - + +
161g SER* 3.0 35.2 + - - +
163g THR* 1.3 84.9 + - - +
165g ALA* 1.3 58.4 + - - +
167g ASP* 3.5 9.0 + - - +
168g LEU* 3.0 30.4 + - - +
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Residues in contact with ALA 165 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14g VAL* 4.3 6.1 - - + +
16g PHE* 3.9 17.0 - - + -
21g VAL* 3.9 22.7 - - + -
160g LEU* 4.2 17.4 - - + +
161g SER 3.0 17.3 + - - +
162g GLN 3.6 4.7 - - - +
164g GLU* 1.3 77.3 - - - +
166g ARG* 1.3 57.7 + - - +
168g LEU* 3.3 3.9 + - - +
169g VAL* 2.9 33.1 + - - +
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Residues in contact with ARG 166 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21g VAL* 4.9 6.7 - - + +
162g GLN* 2.9 25.9 + - + +
163g THR* 3.2 7.6 + - - +
165g ALA* 1.3 73.3 - - - +
167g ASP* 1.3 61.2 + - - +
169g VAL* 3.3 6.0 + - - +
170g GLU* 2.9 61.1 + - - +
189g ILE* 4.1 22.6 - - + +
191g THR* 6.2 0.2 - - - -
200g GLU* 2.6 41.4 + - - -
203g LEU* 3.5 23.8 - - - +
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Residues in contact with ASP 167 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163g THR 2.9 16.2 + - - +
164g GLU* 3.6 8.9 - - - +
166g ARG* 1.3 75.0 - - - +
168g LEU* 1.3 67.2 + - - +
170g GLU* 3.1 9.1 + - - +
171g ARG* 3.0 52.6 + - - +
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Residues in contact with LEU 168 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14g VAL* 5.0 4.0 - - + -
149g LEU* 4.8 4.3 - - + +
150g LEU* 3.7 33.2 - - + +
153g VAL* 3.7 46.4 - - + -
154g LEU* 5.4 0.7 - - + -
160g LEU* 3.9 19.7 - - + -
164g GLU 3.0 15.9 + - - +
165g ALA* 3.4 6.1 - - - +
167g ASP* 1.3 79.5 - - - +
169g VAL* 1.3 64.4 + - - +
171g ARG* 3.3 24.0 + - - +
172g CYS* 3.0 28.8 + - - -
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Residues in contact with VAL 169 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12g LEU* 5.0 11.4 - - + -
14g VAL* 3.9 22.9 - - + +
21g VAL* 4.4 16.2 - - + +
23g ALA* 3.7 30.1 - - + +
150g LEU* 5.5 4.0 - - + -
165g ALA 2.9 19.5 + - - +
166g ARG* 3.5 5.6 - - - +
168g LEU* 1.3 79.0 - - + +
170g GLU* 1.3 58.0 + - - +
172g CYS* 3.3 6.3 + - - +
173g MET* 2.9 37.7 + - + +
187g PHE* 5.1 0.2 - - + -
189g ILE* 3.9 23.1 - - + -
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Residues in contact with GLU 170 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166g ARG* 2.9 49.3 + - - +
167g ASP* 3.1 9.8 + - - +
169g VAL* 1.3 78.2 - - - +
171g ARG* 1.3 57.3 + - + +
173g MET* 3.4 7.3 + - - +
174g ARG* 2.9 37.2 + - - +
187g PHE* 4.1 18.8 - - + -
189g ILE* 4.3 7.7 - - + +
203g LEU* 4.1 12.1 - - - +
204g SER 4.5 8.7 - - - +
205g THR* 4.1 10.3 - - + +
206g GLU* 4.7 8.7 - - - +
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Residues in contact with ARG 171 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149g LEU* 4.9 10.5 - - + +
152g GLU* 4.7 12.1 + - - -
153g VAL* 4.9 7.9 - - - +
167g ASP* 3.0 43.4 + - - +
168g LEU* 3.6 30.9 - - + +
170g GLU* 1.3 76.9 - - + +
172g CYS* 1.3 57.6 + - - +
174g ARG* 3.1 28.7 + - - +
175g VAL* 3.0 32.1 + - - +
140p ASP* 2.7 41.4 + - - +
141p LYS* 5.1 2.6 - - - +
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Residues in contact with CYS 172 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12g LEU* 3.4 22.2 - - + -
146g ALA* 3.8 21.8 - - + +
149g LEU* 4.1 15.5 - - - -
150g LEU* 3.7 34.8 - - - -
168g LEU* 3.0 21.6 + - - +
169g VAL* 3.7 2.2 - - - +
171g ARG* 1.3 72.9 - - - +
173g MET* 1.3 68.3 + - - +
175g VAL* 3.2 10.9 + - - +
176g LEU* 3.0 25.6 + - - +
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Residues in contact with MET 173 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10g SER 5.8 1.6 - - - +
12g LEU* 3.5 24.0 - - + -
23g ALA* 3.7 15.0 - - + +
24g ALA* 4.2 4.9 - - - +
25g ASP* 4.0 21.1 - - + +
169g VAL* 2.9 34.1 + - + +
170g GLU* 3.7 6.1 - - - +
172g CYS* 1.3 76.0 - - - +
174g ARG* 1.3 63.7 - - - +
176g LEU* 3.3 15.9 + - + +
177g TYR* 2.9 22.2 + - - +
184g TYR 6.0 0.7 - - - +
187g PHE* 3.7 40.8 - - + -
205g THR* 4.4 11.9 + - + +
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Residues in contact with ARG 174 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170g GLU* 2.9 24.3 + - - +
171g ARG* 3.3 44.5 - - - +
172g CYS 3.1 0.2 - - - -
173g MET* 1.3 78.7 - - - +
175g VAL* 1.3 63.8 + - + +
177g TYR* 3.0 15.5 + - - +
178g TYR* 3.0 45.1 + - + -
205g THR* 4.0 15.3 - - + +
206g GLU* 3.0 47.5 + - - +
207g THR* 5.1 2.2 - - + +
139p GLU 5.6 2.5 - - - -
140p ASP* 4.9 3.4 + - - -
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Residues in contact with VAL 175 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145g LEU* 4.4 27.6 - - + +
146g ALA* 6.0 0.4 - - - -
149g LEU* 3.8 22.2 - - + -
171g ARG 3.0 19.6 + - - +
172g CYS* 3.5 8.1 - - - +
174g ARG* 1.3 78.0 - - + +
176g LEU* 1.3 62.3 + - + +
178g TYR* 3.0 21.6 + - + +
179g ARG* 3.0 14.9 + - + +
136p ALA* 4.3 30.5 - - + +
139p GLU* 4.5 15.3 - - + +
140p ASP* 4.7 9.4 - - + +
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Residues in contact with LEU 176 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10g SER* 3.8 26.9 - - - +
12g LEU* 4.3 19.5 - - + -
141g TYR 4.2 0.4 - - - -
142g GLY* 3.8 21.8 - - - +
145g LEU* 3.8 35.2 - - + -
146g ALA* 4.7 3.1 - - + +
172g CYS 3.0 16.1 + - - +
173g MET* 3.6 19.7 - - + +
174g ARG 3.2 0.2 - - - -
175g VAL* 1.3 76.6 - - - +
177g TYR* 1.3 58.3 + - - +
180g ASP* 2.8 42.7 + - + +
183g SER* 3.3 10.8 + - - +
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Residues in contact with TYR 177 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173g MET 2.9 14.3 + - - +
174g ARG* 3.0 9.6 + - - +
176g LEU* 1.3 76.9 - - - +
178g TYR* 1.3 65.4 + + - +
180g ASP 4.7 2.3 - - - +
183g SER* 3.6 16.1 + - - -
184g TYR* 3.8 11.9 - + - +
185g ASN* 3.4 45.9 + - + +
205g THR* 4.4 13.2 - - - +
207g THR* 3.6 32.5 - - + -
209g TRP* 4.9 12.6 - + - -
19o ARG* 4.5 20.1 + - - -
26o ILE* 5.0 0.2 - - - +
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Residues in contact with TYR 178 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174g ARG* 3.0 41.0 + - + -
175g VAL* 3.0 10.7 + - - +
177g TYR* 1.3 85.7 - + - +
179g ARG* 1.3 63.1 + - + +
180g ASP 3.8 0.2 - - - -
207g THR* 3.5 24.8 - - + -
208g ASN* 2.6 36.2 + - + +
209g TRP* 4.9 3.6 - + - -
19o ARG* 5.3 0.7 + - - -
26o ILE* 3.6 13.9 - - - +
29o ARG* 2.7 52.3 - - - +
139p GLU* 3.3 49.4 - - + +
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Residues in contact with ARG 179 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141g TYR* 5.1 0.2 - - - -
145g LEU* 4.0 21.4 - - + +
175g VAL* 3.0 15.1 + - + +
178g TYR* 1.3 81.6 - - + +
180g ASP* 1.3 60.6 + - - +
211g ILE* 5.5 1.4 - - - +
25o TYR* 3.6 18.5 + - + -
26o ILE* 2.5 55.4 + - - -
27o ALA* 2.5 34.6 + - - +
28o ASN* 3.5 4.6 + - - +
29o ARG* 3.3 29.9 - - - +
30o VAL* 5.7 0.8 - - - +
122p LEU* 6.1 2.8 - - - +
124p TYR* 4.6 7.9 + - - -
135p MET* 3.7 39.0 - - + +
139p GLU* 2.9 29.8 + - + +
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Residues in contact with ASP 180 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9g THR* 2.9 28.3 + - - +
10g SER* 4.3 4.2 + - - -
141g TYR* 3.4 30.0 - - + -
145g LEU* 4.6 1.3 - - + -
176g LEU* 2.8 35.5 + - + +
177g TYR 4.7 2.4 - - - +
178g TYR 3.8 0.2 - - - -
179g ARG* 1.3 73.1 - - - +
181g ALA* 1.3 62.8 + - - +
182g ARG* 3.1 17.1 + - - +
183g SER* 2.8 38.3 + - - +
19o ARG* 4.8 1.4 + - - -
24o SER* 3.9 4.0 - - - +
26o ILE* 3.8 3.4 - - - +
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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