Contacts of the helix formed by residues 153 - 169 (chain A) in PDB entry 5TBY
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.6 17.5 - - + +
115A TYR* 3.4 25.2 - + - +
117A TYR* 4.7 2.2 + - - -
133A VAL* 3.2 54.8 - - + +
134A TYR* 3.7 15.0 - - - -
138A VAL* 4.3 0.8 - - - +
142A TYR* 3.2 22.3 - - + +
151A PRO 3.0 2.6 + - - -
152A PRO* 1.3 75.1 - - - +
154A ILE* 1.3 78.3 + - + +
155A PHE* 3.1 29.5 + + - -
156A SER* 3.2 13.5 + - - -
157A ILE* 3.6 14.0 + - - +
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Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TYR* 3.3 34.8 - - + +
134A TYR* 4.2 7.0 - - + -
153A HIS* 1.3 80.1 - - + +
155A PHE* 1.3 85.7 + - + +
157A ILE* 2.9 45.5 + - + +
158A SER* 3.2 9.1 + - - +
174A ILE* 6.4 1.6 - - + -
176A ILE* 6.3 1.1 - - + -
187A ASN* 5.0 7.0 - - + +
190A ARG* 5.5 4.5 - - + +
191A VAL* 4.0 35.0 - - + -
194A TYR* 6.3 2.0 - - + -
670A VAL* 5.2 11.2 - - + -
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Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL 3.2 27.4 - - - -
134A TYR* 3.8 20.9 - + - -
138A VAL* 3.9 16.6 - - + -
139A VAL* 3.7 28.5 - - + -
142A TYR* 3.5 17.5 - + + -
153A HIS* 3.1 18.5 + + - -
154A ILE* 1.3 94.6 - - + +
156A SER* 1.3 57.2 + - - +
158A SER* 3.2 8.5 - - - -
159A ASP* 3.1 23.2 + - - +
190A ARG* 5.3 3.1 - - + -
193A GLN* 5.5 3.6 - - - -
194A TYR* 3.5 55.2 - + + +
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Residues in contact with SER 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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117A TYR* 4.2 5.7 + - - -
142A TYR* 3.6 22.5 - - - -
145A LYS* 4.7 5.6 + - - -
146A LYS 3.7 19.6 + - - -
147A ARG* 2.8 40.7 + - - -
150A ALA* 4.3 5.2 - - - +
153A HIS 3.2 6.7 + - - -
154A ILE 3.2 0.6 - - - -
155A PHE* 1.3 75.1 - - - +
157A ILE* 1.3 64.4 + - - +
158A SER 3.1 1.8 - - - -
159A ASP* 4.2 7.0 - - - +
160A ASN* 3.0 15.1 + - - +
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Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TYR* 5.6 3.1 - - + -
117A TYR* 3.8 29.8 - - + -
122A CYS* 3.9 33.7 - - + -
147A ARG* 3.4 15.0 + - - +
153A HIS 3.6 15.3 - - - +
154A ILE* 2.9 30.8 + - + +
156A SER* 1.3 76.4 - - - +
158A SER* 1.3 61.2 + - - +
160A ASN* 4.3 0.2 - - - +
161A ALA* 3.9 15.6 + - - +
174A ILE* 5.1 19.8 - - + +
668A HIS* 5.6 5.0 - - + +
669A PHE 5.4 2.5 - - - +
670A VAL* 4.8 8.1 - - + -
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Residues in contact with SER 158 (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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154A ILE* 3.2 10.2 + - - +
155A PHE 3.2 10.8 - - - -
157A ILE* 1.3 75.4 - - - +
159A ASP* 1.3 66.6 + - - +
161A ALA* 2.9 19.1 + - - +
162A TYR* 3.1 13.0 + - - +
174A ILE* 6.5 0.7 - - - -
191A VAL* 6.0 5.8 - - - -
194A TYR* 4.1 15.0 - - - -
195A PHE* 4.8 10.4 - - - +
198A ILE* 4.1 16.1 - - - +
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Residues in contact with ASP 159 (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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142A TYR* 3.4 6.2 - - - +
144A GLY* 3.0 28.5 + - - -
145A LYS* 3.8 21.0 - - + +
155A PHE 3.1 13.0 + - - +
156A SER* 3.5 5.9 + - - +
158A SER* 1.3 78.1 - - - +
160A ASN* 1.3 65.2 + - - +
162A TYR* 3.3 15.4 + - + +
163A GLN* 3.3 25.6 + - - +
194A TYR* 2.9 22.9 + - - -
198A ILE* 3.4 26.2 - - - +
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Residues in contact with ASN 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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145A LYS 4.5 5.5 + - - -
147A ARG* 2.8 71.6 - - + +
156A SER* 3.0 8.3 + - - +
157A ILE 4.3 0.9 - - - +
159A ASP* 1.3 78.7 - - - +
161A ALA* 1.3 59.8 + - - +
163A GLN* 3.3 3.0 - - - +
164A TYR* 2.6 77.2 + - - -
668A HIS* 5.6 1.9 - - - -
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Residues in contact with ALA 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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157A ILE 3.9 11.2 + - - +
158A SER* 2.9 9.2 + - - +
160A ASN* 1.3 82.6 + - - +
162A TYR* 1.3 57.5 + - - +
164A TYR* 3.4 7.4 + - - +
165A MET* 3.0 30.1 + - - +
172A GLN* 3.9 22.3 - - - +
174A ILE* 5.0 2.0 - - + -
668A HIS* 3.7 32.2 + - + +
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Residues in contact with TYR 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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144A GLY* 6.3 1.1 - - - -
158A SER* 3.1 13.9 + - - +
159A ASP* 3.3 24.5 - - + +
161A ALA* 1.3 75.2 - - - +
163A GLN* 1.3 61.6 + - + +
165A MET* 3.1 14.7 + - + +
166A LEU* 3.0 48.0 + - + +
172A GLN* 4.8 4.2 - - - +
195A PHE* 5.0 11.0 - + - -
198A ILE* 4.5 18.9 + - + -
199A ALA* 4.7 4.5 - - + -
252A PHE* 4.1 22.9 - + - -
256A GLY 2.8 28.4 + - - -
257A LYS* 4.1 16.8 + - - +
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Residues in contact with GLN 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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144A GLY* 5.0 5.5 - - - +
145A LYS 3.7 20.7 - - - +
146A LYS* 4.7 18.3 - - - +
159A ASP* 3.4 8.0 - - - +
160A ASN* 3.3 13.5 - - - +
162A TYR* 1.3 79.1 - - + +
164A TYR* 1.3 80.0 + - + +
166A LEU* 3.2 15.3 + - + +
167A THR* 2.9 39.4 + - + +
774A GLU* 4.1 16.2 + - - -
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Residues in contact with TYR 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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147A ARG* 4.2 7.1 + - - +
160A ASN* 2.6 59.5 + - - -
161A ALA* 3.4 11.7 - - - +
162A TYR 3.2 0.4 - - - -
163A GLN* 1.3 96.9 - - + +
165A MET* 1.3 54.4 + - - +
167A THR* 2.7 23.2 + - - -
168A ASP* 2.8 24.4 + - + +
170A GLU* 5.6 1.8 - - - -
666A HIS* 5.6 8.3 - + + +
668A HIS* 5.4 10.1 - + + -
711A ASN* 5.4 8.1 - - - -
768A GLY* 5.9 1.6 + - - -
771A GLY* 5.6 6.5 - - - -
774A GLU* 5.9 0.4 - - - -
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Residues in contact with MET 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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161A ALA 3.0 13.6 + - - +
162A TYR* 3.2 18.2 - - + +
164A TYR* 1.3 77.1 - - - +
166A LEU* 1.3 78.6 + - + +
169A ARG* 3.1 29.3 + - - +
170A GLU 3.2 32.1 - - - +
171A ASN* 4.3 7.0 - - - +
172A GLN* 4.6 6.1 - - + -
252A PHE* 3.8 35.7 - - + -
455A TYR* 4.4 28.6 - - + -
457A ILE* 4.1 23.8 - - - -
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Residues in contact with LEU 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 TYR* 3.0 44.8 + - + +
163A GLN* 3.2 16.4 + - + +
165A MET* 1.3 93.7 - - + +
167A THR* 1.3 59.0 + - + +
169A ARG* 2.7 27.4 + - - +
255A THR 5.1 4.0 - - - +
256A GLY* 4.1 22.0 - - - -
455A TYR* 5.8 7.4 - - + -
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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 GLN* 2.9 22.2 + - + +
164A TYR* 2.7 24.0 + - + -
166A LEU* 1.3 81.2 - - + +
168A ASP* 1.3 63.3 + - - +
169A ARG* 3.1 25.2 + - - +
721A ARG* 5.5 4.0 - - - +
774A GLU* 4.9 14.8 - - - +
391B ASN* 5.1 4.7 + - - +
393B ALA* 6.2 0.3 - - - +
394B ASP* 3.7 8.7 - - - +
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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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164A TYR* 2.8 15.7 + - + +
167A THR* 1.3 74.0 + - - +
169A ARG* 1.3 68.6 + - - +
170A GLU* 3.0 15.5 + - + +
713A ILE* 3.3 29.4 - - - +
394B ASP* 5.5 0.9 - - - -
397B LYS* 2.2 56.8 + - - +
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Residues in contact with ARG 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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165A MET* 3.1 18.5 + - - +
166A LEU* 2.7 32.9 + - - +
167A THR* 3.1 19.8 + - - +
168A ASP* 1.3 78.9 - - - +
170A GLU* 1.3 63.7 + - - +
171A ASN* 3.2 7.4 + - - +
455A TYR* 4.8 11.5 + - - -
391B ASN* 4.7 4.8 - - - +
394B ASP* 3.0 36.2 + - - +
397B LYS* 4.7 5.8 - - - +
403B ARG* 2.6 52.9 + - + +
604B THR* 5.7 4.0 - - + -
608B LEU* 4.0 22.1 - - + +
611B LYS* 5.8 6.3 - - - +
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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