Contacts of the helix formed by residues 157 - 176 (chain B) in PDB entry 6TOS
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 THR 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 3.7 6.2 - - - +
155B LYS* 4.0 4.3 + - + -
156B SER* 1.3 80.4 + - - +
158B ALA* 1.3 57.6 + - - +
159B ARG* 3.4 23.9 + - - +
160B ARG* 3.0 45.1 + - - +
161B ALA* 3.0 26.3 + - - +
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG 4.3 12.1 - - - +
79B THR* 5.2 1.3 - - - -
80B VAL* 3.8 8.6 - - + +
83B TYR* 3.4 32.8 - - + +
157B THR* 1.3 71.3 - - - +
159B ARG* 1.4 60.5 + - - +
161B ALA* 3.3 9.2 + - - +
162B LEU* 3.3 25.3 + - - +
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B THR* 3.2 24.1 + - - +
158B ALA* 1.4 77.0 - - - +
160B ARG* 1.4 102.4 + - - +
162B LEU* 3.3 24.0 + - + +
163B GLY* 3.6 7.6 + - - -
412B SOG 5.1 0.2 + - - -
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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
----------------------------------------------------------
163A GLY* 6.3 0.9 - - - -
166A LEU* 5.6 9.0 - - - +
155B LYS* 3.0 51.3 + - - +
156B SER* 5.1 2.2 - - - +
157B THR* 3.0 35.3 + - - +
159B ARG* 1.4 103.2 - - - +
161B ALA* 1.4 60.5 + - - +
163B GLY 3.9 0.4 - - - -
164B SER* 2.9 29.6 + - - -
412B SOG 3.4 36.5 + - - +
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 4.2 29.8 - - + +
83B TYR* 4.6 9.6 - - + -
84B PHE* 4.4 9.2 - - + -
156B SER* 5.9 0.6 + - - +
157B THR 3.0 11.9 + - - +
158B ALA* 3.3 14.8 - - - +
159B ARG 3.2 0.4 - - - -
160B ARG* 1.4 76.7 - - - +
162B LEU* 1.4 56.9 + - - +
164B SER* 3.2 8.7 + - - -
165B ILE* 2.8 36.5 + - + +
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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
----------------------------------------------------------
83B TYR* 4.7 21.8 - - + -
158B ALA 3.3 15.7 + - - +
159B ARG* 3.3 15.6 + - + +
161B ALA* 1.4 76.3 - - - +
163B GLY* 1.3 55.7 + - - +
165B ILE* 3.6 21.2 + - + +
166B LEU* 3.1 35.1 + - + +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG 3.6 6.1 + - - -
160B ARG 3.5 6.6 + - - -
161B ALA 3.2 0.6 - - - -
162B LEU* 1.3 76.2 - - - +
164B SER* 1.4 63.0 + - - +
166B LEU* 3.4 10.2 + - - +
167B GLY* 3.1 19.1 + - - -
412B SOG 3.5 34.4 - - - +
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 3.7 22.1 - - - -
139B PHE* 4.0 10.8 - - - -
160B ARG 2.9 17.4 + - - -
161B ALA* 3.4 7.9 - - - -
163B GLY* 1.4 74.2 - - - +
165B ILE* 1.4 55.0 + - - +
167B GLY* 3.2 3.8 + - - -
168B ILE* 3.0 33.5 + - - +
412B SOG 3.0 34.6 + - - +
416B SOG 4.3 4.3 - - - -
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Residues in contact with ILE 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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83B TYR* 3.6 39.9 - - + +
84B PHE* 3.7 20.0 - - + -
87B ASN* 3.4 30.7 - - + +
90B LEU* 5.9 1.8 - - + -
161B ALA* 2.8 26.5 + - + +
162B LEU* 3.7 20.4 - - + +
164B SER* 1.4 74.8 - - - +
166B LEU* 1.3 65.3 + - + +
168B ILE* 3.2 16.6 + - - +
169B TRP* 3.2 26.2 + - + -
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 3.5 31.4 - - + -
162B LEU* 3.1 24.7 + - + +
163B GLY* 3.8 8.7 - - - +
164B SER 3.4 0.4 - - - -
165B ILE* 1.3 78.1 - - + +
167B GLY* 1.3 57.7 + - - +
169B TRP* 3.5 8.1 + - + +
170B ALA* 3.1 22.6 + - - +
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Residues in contact with GLY 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 GLY 3.1 10.4 + - - -
164B SER 3.2 4.0 + - - -
166B LEU* 1.3 75.4 - - - +
168B ILE* 1.4 56.2 + - - +
170B ALA* 3.4 6.7 + - - +
171B VAL* 2.9 36.4 + - - +
412B SOG 3.7 24.2 - - - -
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 4.0 22.4 - - + -
87B ASN* 4.2 2.7 - - - +
132B VAL* 3.7 42.0 - - + +
135B LEU* 3.8 25.7 - - + +
136B THR* 3.9 27.4 - - - +
139B PHE* 4.0 16.4 - - + -
164B SER 3.0 18.8 + - - +
165B ILE* 3.2 12.3 + - - +
167B GLY* 1.4 75.4 - - - +
169B TRP* 1.4 54.3 + - - +
171B VAL* 4.0 2.0 - - - +
172B SER* 2.7 36.6 + - - -
412B SOG 4.4 5.6 - - + -
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Residues in contact with TRP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 4.3 11.0 - - + -
87B ASN* 2.8 30.8 + - - +
90B LEU* 4.4 12.6 - - + +
91B ALA* 4.2 20.6 - - - -
94B LEU* 4.2 21.3 - - + -
128B VAL* 4.0 18.8 - - + -
129B SER* 5.8 0.2 - - - -
132B VAL* 3.7 35.2 - - + -
165B ILE* 3.2 27.8 + - + -
166B LEU* 3.7 12.1 - - + +
167B GLY 3.4 0.2 - - - -
168B ILE* 1.4 74.0 - - - +
170B ALA* 1.3 59.1 + - - +
172B SER* 4.5 2.5 - - - -
173B LEU* 2.9 53.7 + - + +
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 4.0 8.5 - - + +
146A TYR* 2.7 40.4 + - + -
154A PHE* 3.7 29.5 - - + -
166B LEU 3.1 16.9 + - - +
167B GLY* 3.4 9.6 + - - +
169B TRP* 1.3 74.1 - - - +
171B VAL* 1.4 62.3 + - - +
174B ALA* 3.3 8.3 + - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE* 5.3 4.3 - - + -
142A LEU* 3.6 27.1 - - + -
135B LEU* 4.2 18.8 - - + -
167B GLY 2.9 22.0 + - - +
168B ILE 4.0 3.6 - - - +
170B ALA* 1.4 74.5 - - - +
172B SER* 1.3 58.4 + - - +
174B ALA* 3.2 3.1 + - - +
175B ILE* 2.9 53.7 + - + +
405B PGW 4.7 14.4 - - + -
412B SOG 3.7 31.2 - - + -
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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
----------------------------------------------------------
128B VAL* 3.5 7.7 - - - +
131B SER* 2.7 33.2 + - - -
132B VAL* 3.3 32.0 + - - +
135B LEU* 3.8 4.0 - - - +
168B ILE 2.7 22.3 + - - -
169B TRP 3.9 1.6 - - - -
171B VAL* 1.3 72.9 - - - +
173B LEU* 1.3 64.7 + - - +
174B ALA 3.4 0.2 + - - -
175B ILE* 4.2 2.0 - - - -
176B MET* 3.4 29.5 + - - +
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Residues in contact with LEU 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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146A TYR* 3.6 10.1 - - - +
153A LEU* 6.4 0.2 - - + -
154A PHE* 4.0 24.2 - - + -
124B TYR* 2.7 48.4 + - + +
125B LEU* 5.1 5.8 - - + -
128B VAL* 3.8 25.1 - - + -
169B TRP* 2.9 42.9 + - + +
172B SER* 1.3 75.6 - - - +
174B ALA* 1.4 59.0 + - - +
177B VAL* 3.4 7.7 + - - +
408B SOG 4.2 13.6 - - + +
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Residues in contact with ALA 174 (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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142A LEU* 3.6 22.4 - - + -
145A TRP* 3.7 20.6 - - + -
146A TYR* 3.7 0.4 + - - -
170B ALA 3.3 18.6 + - - +
171B VAL 3.2 4.2 + - - +
173B LEU* 1.4 74.5 - - - +
175B ILE* 1.3 62.4 + - + +
176B MET 3.2 6.3 + - - -
177B VAL* 3.3 18.4 + - - +
178B PRO* 4.1 0.7 - - - +
405B PGW 3.6 27.3 - - + +
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 3.9 29.2 - - + +
131B SER* 3.6 19.5 - - - +
135B LEU* 5.2 2.9 - - + -
171B VAL* 2.9 39.4 + - + +
172B SER* 4.1 7.4 - - - +
173B LEU 3.8 0.2 - - - -
174B ALA* 1.3 74.8 - - + +
176B MET* 1.3 68.3 + - + +
177B VAL 3.4 0.7 - - - -
178B PRO* 3.4 13.7 - - - +
215B TYR* 5.3 0.9 + - - -
222B VAL* 4.8 9.0 - - + -
223B THR* 5.8 0.7 - - + -
405B PGW 3.7 68.0 - - + +
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Residues in contact with MET 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TYR* 3.3 15.6 - - + -
127B ALA* 3.6 46.7 - - + +
128B VAL* 3.8 15.9 - - + +
131B SER* 3.6 17.5 - - - -
172B SER 3.4 19.8 + - - +
173B LEU 4.1 0.2 + - - -
174B ALA 3.2 1.0 - - - -
175B ILE* 1.3 85.2 - - + +
177B VAL* 1.4 62.8 + - - +
178B PRO 3.5 1.6 - - - -
179B GLN* 3.2 20.3 - - - +
180B ALA 3.4 1.0 + - - -
215B TYR* 4.7 4.3 - - - -
219B PHE* 3.7 28.3 - - + -
223B THR* 3.7 16.4 - - + -
405B PGW 3.9 13.5 - - + -
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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