Contacts of the helix formed by residues 158 - 177 (chain A) in PDB entry 1BY7
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 PHE 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A PHE* 3.9 10.5 - - + -
132A GLU* 2.8 35.7 + - + +
156A VAL* 3.4 25.5 + - + -
157A ASP* 1.3 74.5 - - - +
159A LEU* 1.3 67.7 + - - +
160A GLU 3.4 0.7 + - - -
162A ALA* 3.3 24.3 + - + +
165A ALA* 3.8 16.6 - - + -
169A ILE* 4.2 7.9 - - + -
190A VAL* 3.7 24.2 - - + -
191A ASP 4.3 1.6 - - - +
192A GLY* 3.6 8.1 - - - -
194A THR* 3.3 54.7 - - + +
195A ARG 3.8 8.3 - - - -
196A MET 4.1 0.7 - - - -
197A VAL* 4.2 19.5 - - + -
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Residues in contact with LEU 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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132A GLU* 3.0 16.6 + - - +
134A SER* 3.8 22.4 - - - +
157A ASP* 3.4 4.2 - - - +
158A PHE* 1.3 79.6 - - - +
160A GLU* 1.3 72.7 + - + +
192A GLY* 3.6 17.6 - - - +
195A ARG* 3.5 35.2 - - - +
346A ARG* 4.1 12.8 - - - +
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Residues in contact with GLU 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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157A ASP* 3.1 24.6 + - - +
158A PHE 4.2 0.2 - - - -
159A LEU* 1.3 93.7 - - + +
161A CYS* 1.3 68.2 + - - +
162A ALA 3.7 1.7 + - - -
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Residues in contact with CYS 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 ASP* 2.9 31.6 + - + +
160A GLU* 1.3 86.7 - - - +
162A ALA* 1.3 67.0 + - - +
163A GLU* 3.3 3.4 - - - -
164A GLU* 3.2 32.8 + - + +
165A ALA* 3.0 17.5 + - - +
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Residues in contact with ALA 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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157A ASP 3.4 4.1 + - - -
158A PHE* 3.3 21.6 + - - +
160A GLU 3.7 1.6 + - - -
161A CYS* 1.3 75.8 - - - +
163A GLU* 1.3 57.3 + - - +
165A ALA* 3.1 7.7 + - - +
166A ARG 2.7 25.1 + - - -
190A VAL* 3.5 13.6 - - + +
191A ASP* 3.4 38.1 - - - +
192A GLY* 3.9 1.1 - - - +
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Residues in contact with GLU 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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161A CYS 3.3 0.8 - - - -
162A ALA* 1.3 76.4 - - - +
164A GLU* 1.4 59.3 + - + +
166A ARG* 2.9 46.2 + - - +
167A LYS* 2.7 57.8 + - - +
187A GLU 3.8 12.9 - - - +
190A VAL 5.3 4.7 + - - +
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Residues in contact with GLU 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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161A CYS* 3.2 32.8 + - + +
163A GLU* 1.4 82.0 - - + +
165A ALA* 1.3 56.9 + - - +
167A LYS* 3.1 10.1 + - - +
168A LYS* 2.9 42.9 + - + +
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Residues in contact with ALA 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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156A VAL* 4.0 16.2 - - + -
157A ASP 4.2 5.2 - - - +
158A PHE* 3.8 28.3 - - + -
161A CYS 3.0 12.6 + - - +
162A ALA* 3.2 10.3 - - - +
164A GLU* 1.3 71.6 - - - +
166A ARG* 1.4 68.8 + - - +
168A LYS* 2.9 16.2 + - - +
169A ILE* 2.7 32.1 + - - +
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Residues in contact with ARG 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 ALA 2.7 14.1 + - - +
163A GLU* 2.9 40.5 + - - +
165A ALA* 1.4 78.1 - - - +
167A LYS* 1.4 79.6 + - - +
169A ILE* 3.3 8.7 + - - +
170A ASN* 3.0 35.7 + - - +
183A ASN* 4.6 9.5 - - - +
185A LEU* 2.9 45.8 + - + -
186A PRO* 3.5 22.3 - - - +
187A GLU* 4.0 22.1 - - - +
188A GLY* 5.5 0.2 - - - -
189A SER* 4.4 5.4 - - - +
190A VAL* 4.2 15.6 - - + +
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Residues in contact with LYS 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 GLU* 2.7 53.2 + - - +
164A GLU* 3.1 8.2 + - - +
166A ARG* 1.4 89.1 - - - +
168A LYS* 1.3 56.0 + - + +
170A ASN* 3.5 6.5 + - - +
171A SER* 3.1 28.8 + - - -
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Residues in contact with LYS 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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130A PHE* 5.1 2.2 - - + -
154A GLN* 4.5 21.3 + - - +
156A VAL* 4.6 18.7 - - + +
157A ASP* 5.2 4.5 - - - +
164A GLU* 2.9 31.1 + - + +
165A ALA* 2.9 14.3 + - - +
167A LYS* 1.3 72.0 - - - +
169A ILE* 1.3 69.0 + - + +
171A SER* 3.4 6.4 + - - +
172A TRP* 3.1 22.7 + - - +
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Residues in contact with ILE 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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130A PHE* 3.6 47.8 - - + -
156A VAL* 4.9 3.6 - - + -
158A PHE* 4.2 13.2 - - + -
165A ALA* 2.7 28.0 + - + +
166A ARG* 3.7 4.5 - - - +
168A LYS* 1.3 74.6 - - - +
170A ASN* 1.3 63.7 + - - +
172A TRP* 3.3 3.5 + - - +
173A VAL* 3.0 26.1 + - + +
185A LEU* 3.8 42.0 - - + -
197A VAL* 3.8 21.1 - - + -
199A VAL* 3.8 9.0 - - + -
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Residues in contact with ASN 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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166A ARG* 3.0 35.7 + - - +
167A LYS* 3.5 6.1 + - - +
168A LYS 3.3 0.2 - - - -
169A ILE* 1.3 76.8 - - - +
171A SER* 1.3 55.2 + - - +
173A VAL* 3.4 4.8 + - - +
174A LYS* 3.0 30.3 + - - +
181A ILE 4.4 0.2 - - - +
182A PRO 3.7 16.3 - - - +
183A ASN* 3.7 17.1 - - - +
184A LEU* 3.5 3.0 + - - +
185A LEU* 2.6 60.4 + - - +
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Residues in contact with SER 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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167A LYS 3.1 17.5 + - - -
168A LYS* 3.4 6.6 + - - -
169A ILE 3.3 0.4 - - - -
170A ASN* 1.3 72.5 - - - +
172A TRP* 1.3 62.6 + - - +
174A LYS* 4.0 7.1 - - - +
175A THR* 2.8 38.7 + - - -
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Residues in contact with TRP 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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126A VAL* 4.2 12.6 - - + -
127A ASN 3.4 32.3 - - - -
128A LYS* 3.5 49.8 - - + +
130A PHE* 4.3 12.6 - + + -
154A GLN* 4.8 7.9 - - - +
168A LYS 3.1 17.1 + - - +
169A ILE 3.3 2.9 + - - +
171A SER* 1.3 79.3 - - - +
173A VAL* 1.3 71.5 + - + +
175A THR* 3.7 5.0 - - + -
176A GLN* 2.9 72.5 + - + +
199A VAL* 3.9 14.4 - - + -
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Residues in contact with VAL 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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126A VAL* 5.7 1.3 - - + -
169A ILE* 3.0 23.9 + - + +
170A ASN 3.8 3.6 - - - +
172A TRP* 1.3 92.7 - - + +
174A LYS* 1.3 67.7 + - - +
175A THR 3.1 0.5 + - - -
176A GLN* 3.2 2.0 + - - -
177A THR* 3.0 30.8 + - + +
181A ILE* 3.6 32.8 - - + +
184A LEU* 3.8 39.9 - - + +
199A VAL* 4.2 9.4 - - + -
201A ALA* 5.2 4.3 - - + -
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Residues in contact with LYS 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 ASN 3.0 18.9 + - - +
171A SER* 4.0 6.5 - - - +
173A VAL* 1.3 75.9 - - - +
175A THR* 1.3 65.7 + - - +
177A THR* 3.3 2.6 + - - -
178A LYS* 3.3 2.1 + - - -
179A GLY* 3.1 35.7 + - - -
181A ILE 3.1 14.6 + - - +
182A PRO* 3.4 37.3 + - + +
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Residues in contact with THR 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 SER* 2.8 32.0 + - - -
172A TRP* 3.7 5.2 - - + -
174A LYS* 1.3 77.9 - - - +
176A GLN* 1.3 67.5 + - - +
178A LYS* 2.8 20.7 + - - +
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Residues in contact with GLN 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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126A VAL* 3.6 36.4 - - + +
172A TRP* 2.9 67.1 + - + +
173A VAL 3.9 2.7 - - - +
175A THR* 1.3 78.9 - - - +
177A THR* 1.3 56.3 + - - +
178A LYS* 3.3 9.4 + - - +
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Residues in contact with THR 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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126A VAL* 4.1 19.7 - - + -
173A VAL* 3.0 21.9 + - + +
174A LYS* 3.3 7.3 + - - -
175A THR 2.9 2.0 + - - -
176A GLN* 1.3 75.6 - - - +
178A LYS* 1.3 72.7 + - - +
180A LYS* 2.8 30.7 + - - +
181A ILE* 3.3 40.4 + - + -
201A ALA* 4.2 11.0 - - + -
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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