Contacts of the helix formed by residues 155 - 175 (chain A) in PDB entry 5JNQ
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 PHE 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.6 48.4 + - + -
153A GLY 3.3 0.8 - - - -
154A ILE* 1.3 92.5 - - + +
156A PHE* 1.4 56.2 + - - +
157A VAL 3.5 0.9 - - - -
158A PRO* 3.5 14.8 - - + -
159A ALA* 2.9 34.7 + - + +
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ALA* 5.2 1.3 - - + -
126A LEU* 4.0 30.5 - - + -
127A LEU* 3.9 32.1 - - + -
134A THR* 3.3 54.3 - - + -
136A MET* 4.9 9.2 - - + -
152A LEU* 4.7 1.5 - - - +
153A GLY* 3.2 29.0 + - - +
154A ILE 3.3 0.2 - - - -
155A PHE* 1.4 76.2 - - - +
157A VAL* 1.3 60.9 + - + +
159A ALA* 3.7 4.3 - - - +
160A LEU* 2.9 39.1 + - + +
246A TYR* 3.9 24.5 + + - -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA* 4.3 15.0 - - + -
127A LEU* 3.7 30.1 - - + -
153A GLY 5.4 1.8 - - - +
154A ILE 4.3 3.8 + - - +
156A PHE* 1.3 75.7 - - + +
158A PRO* 1.4 71.4 - - + +
160A LEU* 3.1 7.6 + - - +
161A PHE* 3.0 52.2 + - + -
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Residues in contact with PRO 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE 3.5 13.0 - - - +
155A PHE* 3.4 28.0 - - + +
157A VAL* 1.4 91.0 - - + +
159A ALA* 1.4 54.8 + - - +
161A PHE* 3.4 8.0 + - + +
162A PHE* 3.1 29.5 + - - +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A MET* 4.6 16.4 - - + -
155A PHE* 2.9 22.8 + - + +
156A PHE* 3.7 5.6 - - - +
158A PRO* 1.4 73.0 - - - +
160A LEU* 1.4 64.2 + - - +
162A PHE* 3.6 6.6 + - - +
163A ILE* 3.2 27.0 + - - +
246A TYR* 3.8 2.2 + - - -
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A THR* 4.1 11.7 - - + +
122A PHE* 4.2 4.9 - - + -
123A ALA* 3.7 38.6 - - + +
126A LEU* 4.2 13.9 - - + -
156A PHE* 2.9 25.9 + - + +
157A VAL* 3.1 6.5 + - - +
159A ALA* 1.4 72.6 - - - +
161A PHE* 1.4 55.1 + - + +
163A ILE* 3.4 2.8 - - - +
164A MET* 2.8 58.8 + - - +
246A TYR* 3.3 44.4 + - + +
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Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 3.3 67.5 - + + -
119A THR* 3.7 26.2 - - + -
120A GLY* 3.7 27.8 - - - -
123A ALA* 4.8 1.8 - - + -
157A VAL* 3.0 46.4 + - + +
158A PRO* 3.8 10.3 - - + +
160A LEU* 1.4 73.9 - - + +
162A PHE* 1.3 56.6 + - - +
164A MET* 4.0 0.2 - - - +
165A LEU* 2.9 47.2 + - + +
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PRO 3.1 17.8 + - - +
159A ALA* 3.8 7.4 - - - +
160A LEU 3.3 0.2 - - - -
161A PHE* 1.3 78.0 - - - +
163A ILE* 1.3 64.1 + - + +
165A LEU* 4.5 4.0 - - - +
166A GLY* 3.2 21.4 + - - -
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A MET* 5.8 0.4 - - + -
159A ALA 3.2 18.0 + - - +
160A LEU 3.4 3.6 - - - +
162A PHE* 1.3 83.4 - - + +
164A MET* 1.4 57.9 + - - +
166A GLY* 3.7 1.0 - - - -
167A THR* 2.8 50.7 + - - +
242A ALA* 5.4 0.7 - - + -
246A TYR* 3.2 32.1 - - + +
251A PRO* 3.4 31.0 - - + +
252A LEU* 5.6 3.1 - - + -
254A ILE* 4.0 16.2 - - + -
255A PRO* 4.8 9.6 - - + -
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Residues in contact with MET 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 3.6 30.5 - - + -
86A PHE* 3.8 18.8 - - + -
118A ILE* 6.0 0.2 - - + -
119A THR* 3.8 28.5 - - + +
122A PHE* 3.8 25.6 - - + -
160A LEU* 2.8 43.4 + - + +
161A PHE 4.0 0.4 - - - +
163A ILE* 1.4 72.6 - - + +
165A LEU* 1.4 57.8 + - - +
167A THR* 4.0 1.0 - - - -
168A ASP* 3.0 30.8 + - - +
238A GLY 5.6 0.2 - - - +
239A GLY* 4.0 3.1 - - - +
242A ALA* 3.8 32.7 - - + +
243A ALA 4.2 0.9 - - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 4.3 22.7 - - + +
115A GLN* 3.4 42.8 - - + +
116A PHE* 4.3 22.0 - - + +
119A THR* 5.4 4.5 - - - +
161A PHE* 2.9 34.0 + - + +
162A PHE* 4.5 3.8 - - - +
164A MET* 1.4 73.0 - - - +
166A GLY* 1.3 59.1 + - - +
168A ASP* 4.6 2.9 - - - -
169A ASN* 2.8 42.9 + - - +
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Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PHE* 3.2 16.2 + - - -
163A ILE* 3.4 3.6 + - - -
165A LEU* 1.3 78.6 - - - +
167A THR* 1.4 51.3 + - - +
169A ASN* 5.0 1.6 - - - -
170A GLY* 2.9 31.7 + - - -
261A TYR* 5.5 0.3 - - - +
265A VAL* 3.8 18.3 - - - +
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Residues in contact with THR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE* 2.8 29.9 + - - +
164A MET 4.0 2.7 - - - -
166A GLY* 1.4 70.2 - - - +
168A ASP* 1.4 56.7 + - - +
170A GLY* 3.3 1.9 + - - -
171A VAL* 2.9 41.1 + - + +
238A GLY 3.7 16.6 - - - +
241A VAL* 3.8 28.3 - - + -
242A ALA* 4.1 11.4 - - - +
254A ILE* 3.5 29.5 - - + +
261A TYR* 4.8 7.1 - - + +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE* 3.3 30.0 - - + -
115A GLN* 2.8 28.1 + - - +
164A MET* 3.0 20.0 + - + +
165A LEU* 4.0 4.5 - - - +
167A THR* 1.4 75.0 - - - +
169A ASN* 1.3 57.3 + - - +
171A VAL* 3.6 2.3 + - - +
172A ASN* 3.1 26.9 + - - +
234A SER 4.5 0.9 - - - +
235A LEU* 2.7 37.6 - - - +
238A GLY* 3.4 10.9 + - - +
239A GLY 3.4 10.0 + - - -
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Residues in contact with ASN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 4.9 5.7 - - - +
112A LEU* 4.1 18.7 - - - +
115A GLN* 3.3 32.1 + - - +
165A LEU* 2.8 34.4 + - - +
166A GLY* 5.0 0.2 - - - -
168A ASP* 1.3 72.2 - - - +
170A GLY* 1.3 60.3 + - - +
172A ASN* 3.2 6.4 + - - +
173A PHE* 2.9 47.6 + - + -
265A VAL* 3.7 17.9 - - + -
401A TUM 5.2 3.3 - - - +
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Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLY 2.9 18.8 + - - -
167A THR 3.3 1.5 + - - -
169A ASN* 1.3 76.8 - - - +
171A VAL* 1.4 53.4 + - - +
173A PHE* 3.5 3.4 + - - +
174A THR* 2.7 32.9 + - - -
261A TYR* 3.3 30.0 - - - +
264A GLU* 3.9 0.9 - - - +
265A VAL* 3.5 11.1 - - - +
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A THR* 2.9 24.4 + - + +
168A ASP 4.0 1.6 - - - +
170A GLY* 1.4 71.7 - - - +
172A ASN* 1.3 64.1 + - - +
174A THR* 3.2 15.6 + - - -
175A ASP* 3.4 6.4 + - - +
181A CYS* 3.7 24.6 - - - -
185A THR* 4.7 2.2 - - + +
234A SER* 3.3 19.5 - - - +
237A LEU* 4.3 7.2 - - + -
238A GLY* 3.7 25.1 - - - +
241A VAL* 4.9 2.7 - - + -
261A TYR* 3.6 40.6 - - + +
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Residues in contact with ASN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 4.2 1.9 - - - +
168A ASP 3.1 19.7 + - - +
169A ASN* 3.5 9.9 - - - +
171A VAL* 1.3 76.5 - - - +
173A PHE* 1.4 63.6 + - - +
175A ASP* 3.4 17.8 + - - +
231A ASP* 2.5 32.1 + - - +
234A SER* 3.5 19.6 + - - -
235A LEU* 3.5 19.3 - - + +
401A TUM 2.8 45.4 + - - +
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASN* 2.9 27.1 + - + +
170A GLY 3.8 4.9 - - - +
171A VAL 3.3 0.2 - - - -
172A ASN* 1.4 78.2 - - - +
174A THR* 1.3 58.2 + - - +
264A GLU* 2.9 35.8 - - + +
265A VAL* 3.7 26.5 - - + -
268A VAL* 3.8 31.2 - - + -
269A ILE* 5.8 2.2 - - + -
288A PRO* 3.9 12.5 - - + +
290A HIS* 3.1 3.6 - - - -
401A TUM 2.7 82.1 + - + -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLY 2.7 19.5 + - - -
171A VAL* 3.2 13.9 + - - -
173A PHE* 1.3 77.1 - - - +
175A ASP* 1.3 54.9 + - - +
176A GLY 2.9 9.4 + - - -
180A LEU* 3.3 35.6 - - + +
181A CYS* 3.9 20.0 - - - -
184A VAL* 4.8 2.0 - - + -
260A ILE* 4.2 17.2 - - + +
261A TYR* 3.7 19.8 - - + -
264A GLU* 3.3 22.5 - - + +
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Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL 3.4 4.6 + - - +
172A ASN 3.4 11.8 + - - +
173A PHE 3.3 1.4 - - - -
174A THR* 1.3 71.7 - - - +
176A GLY* 1.3 56.0 + - - +
177A LEU 4.7 1.8 - - - +
181A CYS* 3.8 19.7 + - + +
221A ASN* 5.7 0.7 + - - +
229A MET* 3.3 32.7 + - - +
230A GLY 3.2 25.5 - - - +
234A SER* 4.0 12.6 - - - -
401A TUM 3.3 53.7 + - - +
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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
------------------------------------------------------------
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