Contacts of the helix formed by residues 170 - 182 (chain A) in PDB entry 6E8Z
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 ASP 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A CYS* 3.3 10.0 - - - +
169A LYS* 1.3 78.6 - - + +
171A PRO* 1.3 74.0 - - - +
172A ALA* 3.0 12.2 + - - +
173A GLN* 2.7 40.0 + - + +
174A GLY* 2.9 20.1 + - - -
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Residues in contact with PRO 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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169A LYS 3.4 9.6 - - - +
170A ASP* 1.3 88.7 - - - +
172A ALA* 1.3 62.3 + - - +
174A GLY* 3.2 2.0 + - - -
175A GLN* 3.1 23.7 + - - +
190A VAL* 6.5 0.9 - - + -
192A GLN* 4.3 18.4 - - + +
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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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170A ASP* 3.0 9.6 + - - +
171A PRO* 1.3 79.6 - - - +
173A GLN* 1.3 61.8 + - - +
175A GLN* 3.5 6.4 + - - +
176A LEU* 3.1 24.0 + - - +
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Residues in contact with GLN 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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88A ILE* 4.7 4.2 - - - +
114A THR* 3.0 39.7 + - + +
115A GLY 5.1 2.6 + - - +
145A SER* 4.5 2.4 + - - +
168A CYS* 3.5 17.7 - - - -
170A ASP* 2.7 29.9 + - + +
172A ALA* 1.3 72.2 - - - +
174A GLY* 1.3 64.4 + - - +
176A LEU* 3.3 24.5 + - - +
177A LEU* 3.0 43.7 + - + +
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Residues in contact with GLY 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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166A ILE* 5.0 1.4 - - - +
168A CYS* 3.5 22.5 - - - -
170A ASP 2.9 13.0 + - - -
171A PRO* 3.2 3.3 + - - -
173A GLN* 1.3 75.1 - - - +
175A GLN* 1.3 57.4 + - - +
177A LEU* 3.2 6.0 + - - +
178A LYS* 2.8 28.8 + - - +
190A VAL* 3.9 21.8 - - - +
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Residues in contact with GLN 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 PRO 3.1 15.4 + - - +
172A ALA* 3.7 6.5 - - - +
173A GLN 3.3 0.2 - - - -
174A GLY* 1.3 74.8 - - - +
176A LEU* 1.3 62.2 + - - +
178A LYS* 3.3 26.3 + - - +
179A GLU* 3.1 59.0 + - - +
190A VAL* 5.0 2.6 - - - +
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Residues in contact with LEU 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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4A LYS* 4.3 33.2 - - + +
31A GLN* 4.3 10.1 - - + -
32A PHE* 3.3 47.3 - - + -
88A ILE* 4.3 9.0 - - + -
172A ALA 3.1 16.9 + - - +
173A GLN* 3.5 24.5 - - - +
174A GLY 3.2 0.2 - - - -
175A GLN* 1.3 74.5 - - - +
177A LEU* 1.3 65.6 + - + +
179A GLU* 3.4 13.8 + - - +
180A LEU* 3.0 17.8 + - - +
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Residues in contact with LEU 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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88A ILE* 4.0 28.0 - - + -
115A GLY 5.4 0.9 - - - +
116A ILE* 4.2 24.0 - - + +
145A SER* 3.8 30.1 - - - +
166A ILE* 4.1 16.4 - - + +
168A CYS* 4.2 4.5 - - + -
173A GLN* 3.0 42.3 + - + +
174A GLY* 3.7 7.0 - - - +
176A LEU* 1.3 77.7 - - + +
178A LYS* 1.3 63.1 + - - +
180A LEU* 3.3 10.1 + - + -
181A MET* 3.2 32.4 + - + +
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Residues in contact with LYS 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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166A ILE* 4.2 2.0 - - - +
174A GLY 2.8 16.5 + - - +
175A GLN* 3.6 29.2 - - - +
176A LEU 3.2 0.2 - - - -
177A LEU* 1.3 76.3 - - - +
179A GLU* 1.3 57.3 + - + +
182A GLN* 2.8 56.1 + - - +
188A ILE* 2.8 46.7 + - + -
189A THR* 4.7 2.6 - - - +
190A VAL* 3.9 16.7 - - + +
348B HIS 2.8 31.3 + - - -
349B MET* 4.8 7.8 + - - -
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Residues in contact with GLU 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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25A ASN* 3.7 8.0 + - - -
29A LEU* 3.3 21.2 - - + +
31A GLN* 3.1 31.4 + - - +
32A PHE* 4.3 0.7 - - + -
175A GLN* 3.1 44.6 + - - +
176A LEU* 3.6 18.4 - - - +
177A LEU 3.3 0.2 - - - -
178A LYS* 1.3 76.4 - - + +
180A LEU* 1.3 63.5 + - - +
181A MET 3.3 0.3 + - - -
182A GLN* 4.0 4.9 + - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.8 23.3 - - + -
22A VAL* 4.0 30.9 - - + +
25A ASN* 3.0 22.0 + - - +
26A ALA* 4.5 6.1 - - + +
32A PHE* 3.5 36.1 - - + -
88A ILE* 4.5 13.9 - - + -
90A ILE* 4.2 21.5 - - + -
176A LEU 3.0 18.1 + - - +
177A LEU* 3.7 10.8 - - + +
178A LYS 3.3 0.4 - - - -
179A GLU* 1.3 78.7 - - - +
181A MET* 1.3 66.3 + - + +
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Residues in contact with MET 181 (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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18A ILE* 3.3 47.6 - - + +
21A ILE* 3.2 25.4 - - + +
22A VAL* 3.6 12.8 - - + -
25A ASN* 3.8 2.0 - - - +
90A ILE* 4.9 11.4 - - + -
116A ILE* 5.2 9.4 - - - -
118A LEU* 5.1 4.3 - - + -
147A LEU* 3.7 24.0 - - + -
166A ILE* 5.1 1.3 - - + -
177A LEU* 3.2 19.9 + - + +
180A LEU* 1.3 94.1 - - + +
182A GLN* 1.3 61.5 + - - +
186A PHE* 3.4 17.4 - - + -
188A ILE* 3.6 14.6 - - + -
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Residues in contact with GLN 182 (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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25A ASN* 3.0 19.4 + - - +
178A LYS* 2.8 50.5 + - + +
179A GLU* 4.0 3.9 + - - +
180A LEU 3.8 0.4 - - - -
181A MET* 1.3 78.2 - - - +
183A THR* 1.3 62.4 + - - +
186A PHE 3.5 11.4 - - - +
187A ARG* 3.3 39.5 + - - +
188A ILE* 3.2 28.5 + - + +
348B HIS* 4.2 2.0 + - - +
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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