Contacts of the helix formed by residues 167 - 179 (chain B) in PDB entry 6S6A
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 GLU 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B ASP* 1.3 86.3 - - - +
168B THR* 1.3 72.0 + - + +
169B LEU 3.3 0.7 - - - -
170B TYR* 3.1 14.0 + - - +
171B LYS 3.4 0.9 + - - -
226B HIS* 4.7 8.6 - - + +
229B GLU* 3.1 51.2 - - + +
230B LYS* 3.7 36.0 - - + +
233B ASN* 3.7 12.9 - - - +
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B MET* 5.8 0.5 - - - +
160B PHE* 5.8 0.2 - - - +
161B ARG* 3.4 37.3 + - + +
162B THR* 3.4 6.7 + - - +
163B SER* 3.1 17.5 + - - -
166B ASP* 2.7 31.3 + - - +
167B GLU* 1.3 81.5 - - + +
169B LEU* 1.3 64.8 + - - +
171B LYS* 3.1 19.8 + - + +
172B ALA* 3.3 13.0 + - - +
226B HIS* 6.3 2.2 - - + +
229B GLU* 5.1 0.2 - - - -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B MET* 3.4 40.2 - - + -
26B ILE* 3.8 32.3 - - + -
27B ILE* 4.1 12.6 - - + -
127B HIS* 4.7 4.0 - - + -
162B THR* 3.9 12.3 - - + +
163B SER 3.3 18.2 + - - +
164B ILE* 4.4 16.2 - - + +
166B ASP 3.8 4.7 + - - +
167B GLU 3.3 0.4 - - - -
168B THR* 1.3 79.0 + - - +
170B TYR* 1.3 65.6 + - + +
172B ALA* 3.4 1.7 + - - +
173B TRP* 3.2 51.5 + - + +
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Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.6 29.7 + - + +
27B ILE* 3.8 21.9 - - + +
166B ASP 4.8 3.1 - - - -
167B GLU 3.1 10.7 + - - +
169B LEU* 1.3 79.4 - - + +
171B LYS* 1.3 65.4 + - - +
173B TRP 4.6 0.4 - - - +
174B SER* 2.9 29.5 + - - -
210B THR 3.7 20.0 + - - -
212B LEU* 3.6 19.2 - - + +
229B GLU* 4.1 17.9 - - + +
232B SER* 3.8 22.2 - - - -
233B ASN* 4.4 32.3 - - + -
236B LYS* 3.4 29.7 + - + +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 4.3 20.1 - - + -
168B THR* 3.1 13.4 + - + +
170B TYR* 1.3 73.1 - - - +
172B ALA* 1.3 57.0 + - - +
174B SER* 3.7 0.7 - - - -
175B SER* 2.7 48.4 + - - -
226B HIS* 5.0 8.7 - - + +
229B GLU* 3.3 42.7 - - + +
403B 9JE 4.2 7.9 + - - +
354C TYR* 3.6 21.2 - - + -
355C ASN* 2.8 29.7 + - - +
358C CYS* 4.7 13.0 - - - -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 3.8 11.9 - - + -
160B PHE* 3.7 28.4 - - + -
162B THR* 3.6 26.9 - - + -
168B THR 3.3 2.7 + - - +
169B LEU 3.6 8.3 - - - +
170B TYR 3.2 1.0 - - - -
171B LYS* 1.3 80.0 - - - +
173B TRP* 1.4 62.0 + - + +
175B SER* 3.3 2.4 + - - -
176B ILE* 2.9 34.9 + - - +
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Residues in contact with TRP 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 5.3 1.1 - - + -
12B LEU* 4.3 24.7 - - + -
23B MET* 3.6 31.9 - - + +
24B ARG* 5.0 2.7 - - - -
27B ILE* 3.8 27.6 - - + -
28B PHE* 3.7 34.1 - + - -
60B LEU* 4.6 9.4 - - + -
89B ILE* 3.6 36.1 - - + -
125B LEU* 4.4 6.3 - - + +
169B LEU* 3.2 51.8 + - + +
172B ALA* 1.4 76.5 - - + +
174B SER* 1.3 60.3 + - - +
176B ILE* 3.3 9.8 + - + +
177B VAL* 3.0 41.2 + - + +
212B LEU* 4.1 9.4 - - + -
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B TYR* 2.9 21.0 + - - -
171B LYS 3.7 3.1 - - - -
173B TRP* 1.3 78.0 - - - +
175B SER* 1.3 56.3 + - - -
177B VAL* 4.0 1.3 - - - +
178B TYR* 3.0 31.6 + - - +
212B LEU* 3.8 20.4 - - - +
213B VAL* 3.0 30.5 + - - +
232B SER* 6.1 0.2 - - - -
403B 9JE 3.3 20.1 + - - +
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 3.6 23.2 - - - -
171B LYS* 2.7 26.6 + - - -
172B ALA 3.5 4.0 - - - -
174B SER* 1.3 74.5 - - - +
176B ILE* 1.3 63.5 + - - +
178B TYR* 3.8 5.6 + - - +
179B GLN* 2.7 37.5 + - - +
403B 9JE 3.9 8.3 + - - -
253C ASN 6.0 0.4 - - - -
351C LEU* 3.7 25.8 - - - +
355C ASN* 5.2 0.3 + - - -
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Residues in contact with ILE 176 (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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10B VAL* 5.6 1.1 - - + -
87B VAL* 4.1 25.6 - - + -
89B ILE* 4.2 30.3 - - + -
123B PHE* 3.6 46.2 - - + -
125B LEU* 4.8 7.0 - - + -
160B PHE* 4.4 4.9 - - + -
172B ALA* 2.9 27.4 + - + +
173B TRP* 3.3 15.5 + - + +
174B SER 3.2 0.2 - - - -
175B SER* 1.3 78.6 - - - +
177B VAL* 1.3 62.1 + - + +
179B GLN* 3.0 23.4 + - - +
180B LEU* 3.8 13.6 + - + +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 4.5 9.0 - - + -
52B PHE* 3.4 42.6 - - + -
56B LEU* 4.9 2.7 - - + -
58B LEU* 4.2 22.7 - - + -
173B TRP* 3.0 25.9 + - + +
174B SER 4.1 2.0 - - - +
176B ILE* 1.3 75.1 - - + +
178B TYR* 1.3 58.3 + - - +
179B GLN 3.0 1.8 - - - -
180B LEU* 2.8 30.3 + - + +
181B ILE* 3.2 14.3 + - + +
212B LEU* 3.9 17.0 - - + -
214B ILE* 5.2 1.1 - - + -
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Residues in contact with TYR 178 (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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174B SER 3.0 19.1 + - - +
175B SER* 3.9 5.8 - - - +
177B VAL* 1.3 77.2 - - - +
179B GLN* 1.3 61.4 + - + +
180B LEU 3.2 0.9 + - - -
181B ILE* 3.5 24.4 + - + +
184B VAL* 3.4 23.6 - - + +
188B GLU* 2.5 32.6 + - - -
213B VAL 5.1 2.0 - - - +
214B ILE* 3.3 23.1 - - - +
403B 9JE 3.3 32.8 - - + -
348C ARG* 3.4 41.6 - - + +
350C GLY 3.5 2.3 + - - -
351C LEU* 3.4 35.2 - - + -
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Residues in contact with GLN 179 (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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8B LYS* 4.4 2.9 + - - -
121B LYS* 3.9 30.7 + - + +
123B PHE* 3.8 28.9 - - + -
160B PHE* 5.6 0.6 - - - -
175B SER* 2.7 27.7 + - - +
176B ILE 3.0 10.5 + - - +
178B TYR* 1.3 79.2 - - + +
180B LEU* 1.3 66.6 + - - +
181B ILE 3.6 1.3 - - - +
253C ASN* 4.6 7.5 + - - +
255C GLY* 5.8 1.6 + - - -
348C ARG* 3.7 34.1 + - - +
351C LEU* 3.7 24.4 - - + +
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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