Contacts of the helix formed by residues 167 - 179 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ASP* 1.3 82.8 - - - +
168A THR* 1.3 64.5 + - + +
169A LEU 3.1 2.7 - - - -
170A TYR* 2.8 28.6 + - - +
171A LYS 3.1 8.8 + - - -
226A HIS* 4.9 4.3 - - + +
229A GLU* 3.5 34.4 - - + +
230A LYS* 3.6 39.2 - - + +
233A ASN* 4.2 16.8 + - + +
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Residues in contact with THR 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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129A MET* 6.0 0.2 - - - +
160A PHE* 5.6 0.3 - - - +
161A ARG* 3.3 38.0 + - + +
162A THR* 3.4 13.2 - - - +
163A SER* 3.2 16.5 + - - -
166A ASP* 2.6 29.4 + - - +
167A GLU* 1.3 83.4 - - + +
169A LEU* 1.3 58.7 + - - +
171A LYS* 3.4 12.0 + - + +
172A ALA* 3.2 17.2 + - - +
229A GLU* 5.4 1.1 - - - +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A MET* 4.0 22.9 - - + -
26A ILE* 4.1 29.4 - - + -
27A ILE* 4.0 16.6 - - + -
127A HIS* 4.7 3.4 - - + -
162A THR* 4.1 17.3 - - + -
163A SER 3.4 15.1 + - - +
164A ILE* 4.2 23.6 - - + +
166A ASP 3.4 7.4 + - - +
167A GLU 3.0 1.6 + - - -
168A THR* 1.3 79.1 + - - +
170A TYR* 1.3 60.2 + - + +
172A ALA* 3.4 3.5 + - - +
173A TRP* 3.0 56.2 + - + +
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Residues in contact with TYR 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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26A ILE* 3.6 30.6 + - + +
27A ILE* 3.6 24.0 - - + -
166A ASP 4.5 6.3 - - - -
167A GLU 2.8 15.5 + - - +
169A LEU* 1.3 73.7 - - + +
171A LYS* 1.3 56.8 + - - +
173A TRP 4.6 0.4 - - - +
174A SER* 2.8 37.2 + - - +
210A THR 3.9 19.5 - - - -
212A LEU* 4.1 13.7 - - + -
229A GLU* 4.0 17.7 - - + +
232A SER* 3.9 24.0 - - - -
233A ASN* 3.4 30.3 - - + -
236A LYS* 3.2 29.6 - - + +
237A GLN* 5.4 0.2 - - - -
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Residues in contact with LYS 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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160A PHE* 4.4 17.9 - - + -
167A GLU 3.1 5.9 + - - -
168A THR* 3.5 17.7 - - + +
169A LEU 3.3 0.4 - - - -
170A TYR* 1.3 77.7 - - - +
172A ALA* 1.3 64.6 + - - +
174A SER* 3.8 1.4 - - - -
175A SER* 3.2 32.8 + - - -
225A VAL 5.3 3.6 + - - -
226A HIS* 4.4 14.0 + - + +
229A GLU* 3.2 36.1 + - + +
403A 9JE 3.6 27.9 - - - -
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Residues in contact with ALA 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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125A LEU* 3.7 20.6 - - + -
160A PHE* 3.8 21.8 - - + -
162A THR* 3.5 30.5 - - + -
168A THR 3.2 3.0 + - - +
169A LEU 3.7 3.6 - - - +
171A LYS* 1.3 77.5 - - - +
173A TRP* 1.3 63.5 + - + +
175A SER* 3.1 5.0 + - - -
176A ILE* 3.0 32.1 + - + +
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Residues in contact with TRP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.4 2.5 - - + -
12A LEU* 4.4 19.1 - - + -
23A MET* 3.6 39.8 - - + +
24A ARG* 5.1 2.7 - - - -
27A ILE* 4.0 17.9 - - + -
28A PHE* 3.4 37.7 - + - -
60A LEU* 4.8 10.3 - - + -
89A ILE* 3.2 36.1 - - + -
125A LEU* 4.1 4.9 - - + +
169A LEU* 3.0 38.5 + - + +
172A ALA* 1.3 75.3 - - + +
174A SER* 1.3 68.0 + - - +
176A ILE* 3.8 15.4 - - + +
177A VAL* 2.9 31.6 + - + +
212A LEU* 3.9 15.9 - - + -
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Residues in contact with SER 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 TYR* 2.8 24.7 + - - +
171A LYS 3.8 1.3 - - - -
173A TRP* 1.3 77.6 - - - +
175A SER* 1.3 60.6 + - - -
177A VAL* 3.3 1.8 + - - +
178A TYR* 3.0 24.1 + - - +
212A LEU* 3.4 21.7 - - - +
213A VAL* 3.4 34.3 + - - +
229A GLU* 5.9 1.0 - - - -
232A SER* 4.7 2.3 + - - -
403A 9JE 3.7 25.7 + - - -
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Residues in contact with SER 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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123A PHE* 4.7 4.0 - - - -
160A PHE* 3.6 29.9 - - - -
171A LYS* 3.2 23.4 + - - +
172A ALA 3.1 10.2 + - - -
174A SER* 1.3 74.2 - - - +
176A ILE* 1.3 65.7 + - - +
178A TYR* 3.5 13.3 + - - +
179A GLN* 3.5 18.2 - - - +
403A 9JE 4.6 8.8 - - - +
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Residues in contact with ILE 176 (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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10A VAL* 5.3 2.0 - - + -
87A VAL* 4.4 15.9 - - + -
89A ILE* 3.9 45.3 - - + -
123A PHE* 3.6 39.0 - - + -
125A LEU* 4.8 8.3 - - + -
160A PHE* 5.8 0.4 - - + -
172A ALA 3.0 26.0 + - - +
173A TRP* 3.8 18.8 - - + +
175A SER* 1.3 75.0 - - - +
177A VAL* 1.3 70.4 - - + +
179A GLN* 3.2 17.7 + - - +
180A LEU* 3.8 14.4 + - + +
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Residues in contact with VAL 177 (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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28A PHE* 4.7 8.5 - - + -
52A PHE* 3.2 43.5 - - + -
56A LEU* 5.3 2.0 - - + -
58A LEU* 4.1 24.9 - - + -
173A TRP* 2.9 23.0 + - + +
174A SER 4.1 2.0 - - - +
176A ILE* 1.3 85.2 - - + +
178A TYR* 1.3 54.3 + - - +
180A LEU* 2.9 25.4 + - + +
181A ILE* 3.2 15.9 + - + +
212A LEU* 3.9 16.8 - - + -
213A VAL 6.1 0.4 - - - +
214A ILE* 5.2 2.0 - - + -
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Residues in contact with TYR 178 (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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174A SER 3.0 13.1 + - - +
175A SER* 3.5 11.9 - - - +
176A ILE 3.3 0.4 + - - -
177A VAL* 1.3 76.2 - - - +
179A GLN* 1.3 69.9 + - + +
180A LEU 3.4 0.9 + - - -
181A ILE* 3.7 14.0 + - + +
184A VAL* 3.5 42.3 + - + +
185A GLN* 5.6 1.9 - - - +
188A GLU* 2.6 37.4 + - - +
213A VAL 5.8 0.9 + - - -
214A ILE* 3.4 29.6 - - - -
403A 9JE 3.7 28.9 - - + -
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Residues in contact with GLN 179 (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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8A LYS* 4.8 2.6 + - - -
87A VAL* 6.1 0.2 - - + -
121A LYS* 3.6 44.6 + - + +
123A PHE* 4.2 17.7 - - + -
175A SER 3.5 14.4 - - - +
176A ILE 3.2 9.1 + - - +
177A VAL 3.1 1.0 - - - -
178A TYR* 1.3 84.8 - - + +
180A LEU* 1.3 64.8 + - + +
181A ILE 4.9 1.8 - - - +
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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