Contacts of the helix formed by residues 159 - 178 (chain A) in PDB entry 1L7R
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 SER 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A PRO 3.3 22.8 + - - -
151A TRP 2.8 12.2 + - - +
152A TYR 2.8 23.7 + - - -
157A ALA 3.5 0.6 + - - -
158A LEU* 1.3 68.6 - - - +
160A VAL* 1.3 65.2 + - - +
161A GLU* 3.3 3.4 - - - -
162A ALA* 3.1 10.0 + - - -
163A LEU* 3.0 20.6 + - - +
531A LYS* 3.2 25.8 + - - -
532A TYR* 3.8 12.2 - - - -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 2.9 16.8 + - + -
159A SER* 1.3 74.8 - - - +
161A GLU* 1.3 65.2 + - - +
163A LEU* 3.3 4.2 + - + +
164A LEU* 3.0 35.3 + - + +
203A ALA* 3.7 30.5 - - + +
208A LEU* 3.8 26.5 - - + -
529A PHE* 4.2 2.7 - - + -
530A PRO* 3.2 18.4 - - + +
531A LYS 4.0 1.2 + - - -
533A ASP* 3.9 29.6 - - + +
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 1.3 76.6 - - - +
162A ALA* 1.3 69.9 + - - +
165A GLY* 3.0 22.5 + - - -
199A VAL* 3.7 25.6 - - + +
203A ALA* 5.3 0.7 - - - -
405A THR 4.5 0.2 - - - +
406A LEU* 3.5 26.7 - - + +
407A LEU* 2.8 27.5 + - - +
408A PHE* 2.8 27.1 + - - -
409A HIS* 2.9 9.9 + - + -
530A PRO* 3.1 34.8 + - + +
531A LYS* 3.8 12.4 + - - +
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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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150A PRO 3.7 20.9 - - - +
151A TRP* 3.6 6.8 - - + -
159A SER* 3.1 15.5 + - - +
161A GLU* 1.3 90.2 - - - +
163A LEU* 1.3 61.8 + - - +
166A TRP* 3.0 28.9 + - - +
407A LEU* 3.7 22.4 - - + -
408A PHE* 3.3 11.7 - - - -
531A LYS* 6.0 1.1 - - - +
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Residues in contact with LEU 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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151A TRP* 3.8 21.5 - - + -
158A LEU* 4.2 12.8 - - + -
159A SER 3.0 12.1 + - - +
160A VAL* 3.7 9.9 - - + +
162A ALA* 1.3 78.3 - - - +
164A LEU* 1.3 62.2 + - + +
166A TRP* 4.0 2.0 - - + +
167A SER* 2.7 39.9 + - - +
220A TRP* 5.4 2.0 - - + -
221A VAL* 3.7 25.1 - - + -
225A VAL* 3.6 35.9 - - + -
226A VAL* 3.5 31.2 - - + -
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Residues in contact with LEU 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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160A VAL* 3.0 21.3 + - + +
161A GLU 4.4 1.3 - - - +
163A LEU* 1.3 85.6 - - + +
165A GLY* 1.3 62.6 + - - +
167A SER* 3.4 1.7 + - - -
168A ALA* 3.0 25.6 + - - +
195A ILE* 4.2 11.9 - - + +
199A VAL* 4.4 6.7 - - + +
202A ALA* 3.7 14.6 - - + +
203A ALA* 3.5 43.3 - - + +
208A LEU* 4.8 5.8 - - + -
211A GLN* 4.1 20.2 - - + +
214A LEU* 3.6 28.2 - - + +
221A VAL* 5.4 2.7 - - + -
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Residues in contact with GLY 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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161A GLU 3.0 11.9 + - - -
164A LEU* 1.3 77.9 - - - +
166A TRP* 1.3 60.7 + - - +
168A ALA* 3.3 3.6 + - - +
169A LEU* 3.0 27.2 + - - +
195A ILE* 5.3 0.7 - - - -
196A LEU* 3.8 11.5 - - - +
199A VAL* 4.6 5.7 - - - +
408A PHE* 3.5 30.1 - - - -
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Residues in contact with TRP 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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44A PHE* 4.3 14.0 - + - -
84A PHE* 4.5 0.4 - + - -
86A PRO* 3.7 36.6 - - + -
87A HIS* 5.0 1.1 - + - -
118A TYR* 3.5 33.4 - + - +
151A TRP* 3.4 39.0 - + + -
162A ALA 3.0 19.9 + - - +
163A LEU* 4.0 2.0 - - + +
165A GLY* 1.3 73.4 - - - +
167A SER* 1.3 71.8 + - - +
169A LEU* 3.2 6.0 + - + +
170A ILE* 2.8 65.7 + - + +
218A ILE* 5.6 3.6 - - + -
220A TRP* 4.2 7.9 - + - -
408A PHE* 3.2 22.4 - + + -
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Residues in contact with SER 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 LEU* 2.7 26.0 + - - +
164A LEU 3.7 4.0 - - - -
166A TRP* 1.3 84.0 - - - +
168A ALA* 1.3 53.6 + - - +
171A GLY* 2.7 32.2 + - - -
214A LEU* 4.0 27.3 - - - +
218A ILE* 3.6 19.0 - - - +
221A VAL* 3.3 25.8 - - - +
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Residues in contact with ALA 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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164A LEU 3.0 17.9 + - - +
165A GLY 3.6 4.5 - - - +
167A SER* 1.3 77.9 - - - +
169A LEU* 1.3 57.6 + - - +
171A GLY* 3.7 0.5 - - - -
172A THR* 2.9 33.1 + - - -
192A LEU* 4.0 29.8 - - + +
195A ILE* 4.3 10.1 - - + -
196A LEU* 3.9 23.6 - - + -
214A LEU* 3.9 3.1 - - + +
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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
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44A PHE* 4.5 20.8 - - + -
165A GLY 3.0 14.9 + - - +
166A TRP* 3.2 8.7 + - + +
168A ALA* 1.3 76.4 - - - +
170A ILE* 1.3 61.8 + - - +
172A THR* 3.3 8.9 + - - +
173A GLY* 3.1 17.3 + - - -
196A LEU* 3.7 27.6 - - + -
408A PHE* 3.3 39.3 - - + -
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Residues in contact with ILE 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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43A PRO* 4.9 10.1 - - + +
44A PHE* 4.3 21.3 - - + -
77A LEU* 5.2 5.1 - - + +
84A PHE* 3.5 31.4 - - + -
118A TYR* 5.1 0.2 - - + -
166A TRP* 2.8 64.3 + - + +
167A SER* 4.7 0.2 - - - -
169A LEU* 1.3 73.6 - - - +
171A GLY* 1.3 55.8 + - - +
173A GLY* 2.9 4.2 + - - +
174A LEU* 2.7 39.4 + - + +
218A ILE* 3.4 23.3 - - + -
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Residues in contact with GLY 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 SER 2.7 23.2 + - - -
168A ALA* 3.7 1.6 - - - -
169A LEU 3.2 0.4 - - - -
170A ILE* 1.3 74.1 - - - +
172A THR* 1.3 60.9 + - - +
174A LEU* 3.2 8.0 + - - +
175A ILE* 3.1 27.7 + - - +
192A LEU* 3.9 7.4 - - - -
214A LEU* 6.0 0.2 - - - -
217A LEU* 4.3 16.7 - - - +
218A ILE* 4.1 9.6 - - - -
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Residues in contact with THR 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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168A ALA 2.9 15.3 + - - -
169A LEU* 3.4 13.0 - - - +
170A ILE 3.1 0.2 - - - -
171A GLY* 1.3 75.0 - - - +
173A GLY* 1.3 63.9 + - - +
175A ILE 3.4 1.6 + - - -
176A THR* 3.0 29.8 + - - +
189A PHE* 3.7 25.5 - - + -
192A LEU* 3.5 22.8 - - - +
196A LEU* 5.0 6.2 - - - +
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Residues in contact with GLY 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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43A PRO 6.1 0.4 - - - -
44A PHE* 5.8 5.4 - - - -
77A LEU* 5.0 3.1 - - - -
78A PHE* 4.2 15.4 - - - -
169A LEU 3.1 7.0 + - - -
170A ILE* 2.9 8.0 + - - -
172A THR* 1.3 78.8 - - - +
174A LEU* 1.3 54.3 + - - +
176A THR* 3.1 8.4 + - - -
177A SER* 2.8 41.6 + - - -
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Residues in contact with LEU 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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76A GLY 4.5 3.8 - - - +
77A LEU* 3.3 28.2 - - + +
84A PHE* 3.8 22.9 - - + -
170A ILE* 2.7 22.5 + - + +
171A GLY* 3.5 9.0 - - - +
173A GLY* 1.3 73.4 - - - +
175A ILE* 1.3 63.3 + - + +
177A SER* 3.4 6.4 + - - -
178A ARG* 3.1 27.7 + - - +
217A LEU* 3.7 15.0 - - + +
218A ILE* 3.4 37.7 - - + -
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Residues in contact with ILE 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 GLY 3.1 10.2 + - - +
172A THR 3.7 3.1 - - - +
174A LEU* 1.3 76.8 - - + +
176A THR* 1.3 58.5 + - - +
178A ARG* 3.0 43.4 - - - +
185A ASP* 3.5 29.1 - - + +
188A ASP* 3.6 33.9 - - + +
189A PHE* 3.2 35.2 - - + -
192A LEU* 3.9 20.6 - - + -
217A LEU* 4.4 11.2 - - + -
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Residues in contact with THR 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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78A PHE* 4.0 18.6 - - + -
172A THR* 3.0 19.4 + - - +
173A GLY* 3.5 10.7 - - - -
175A ILE* 1.3 79.6 - - - +
177A SER* 1.3 58.8 + - - +
178A ARG 3.1 5.6 + - - +
189A PHE* 3.8 14.4 - - - -
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Residues in contact with SER 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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76A GLY 5.0 2.7 - - - -
77A LEU* 4.1 7.4 - - - +
78A PHE* 3.0 63.3 + - - +
173A GLY 2.8 26.8 + - - -
174A LEU* 3.8 8.1 - - - -
176A THR* 1.3 71.5 - - - +
178A ARG* 1.3 65.2 + - - +
179A SER* 3.4 2.9 + - - -
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Residues in contact with ARG 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 LEU* 3.1 13.7 + - - +
175A ILE* 3.0 46.2 + - - +
176A THR 3.1 6.4 - - - +
177A SER* 1.3 78.3 - - - +
179A SER* 1.3 72.1 + - - +
180A ASP* 3.2 26.2 + - - +
181A ALA* 4.9 1.6 + - - +
182A ARG* 2.9 57.3 - - - +
185A ASP* 3.2 25.5 + - - +
188A ASP* 5.7 0.6 + - - -
217A LEU* 4.6 12.5 - - - +
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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
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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