Contacts of the helix formed by residues 162 - 178 (chain A) in PDB entry 1O1L
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 HIS 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A LYS 4.7 5.8 - - - -
159A VAL* 3.0 25.3 + - - +
161A ALA* 1.3 82.7 - - + +
163A ALA* 1.3 63.7 + - - +
164A GLY 3.3 1.1 - - - -
165A GLU* 3.1 29.0 + - + +
166A TYR* 2.9 56.9 + - + -
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Residues in contact with ALA 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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156A TRP* 4.5 8.4 - - + +
159A VAL* 3.6 17.8 - - + +
160A GLY 3.3 14.8 + - - +
161A ALA 3.1 2.9 - - - +
162A HIS* 1.3 76.1 - - - +
164A GLY* 1.3 57.9 + - - +
166A TYR* 3.5 1.7 + - - +
167A GLY 2.9 23.2 + - - -
202A LYS* 5.1 7.0 - - - +
205A ALA* 3.1 24.4 - - + +
206A ASP* 5.4 1.1 - - - +
209A THR* 4.3 15.5 - - - +
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Residues in contact with GLY 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 ALA 4.4 3.4 + - - -
162A HIS 3.3 0.4 - - - -
163A ALA* 1.3 76.0 - - - +
165A GLU* 1.3 64.1 + - - +
167A GLY* 3.1 2.6 + - - -
168A ALA* 3.0 23.6 + - - +
198A LYS 5.0 0.3 - - - +
201A GLY 4.2 4.0 - - - -
202A LYS* 3.7 42.4 + - - +
205A ALA* 4.1 0.2 - - - -
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Residues in contact with GLU 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 ALA 5.2 0.8 + - - +
162A HIS* 3.1 32.8 + - - +
164A GLY* 1.3 74.2 - - - +
166A TYR* 1.3 80.0 + - + +
168A ALA* 3.4 7.8 + - - +
169A GLU* 3.2 21.5 + - - +
254A HIS* 4.8 5.4 - - - -
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Residues in contact with TYR 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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159A VAL* 3.7 31.6 - - + -
162A HIS* 2.9 46.9 + + + +
163A ALA* 4.0 3.4 - - - +
165A GLU* 1.3 88.2 - - + +
167A GLY* 1.3 65.4 + - - +
169A GLU* 3.2 2.6 + - - -
170A ALA* 2.9 24.3 + - - +
247A LEU* 4.9 2.9 - - + +
250A THR* 3.5 20.5 - - + +
251A LEU* 4.3 18.4 - - + -
254A HIS* 3.4 57.0 + + + +
255A LEU* 5.5 4.9 - - + +
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Residues in contact with GLY 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 ALA 2.9 16.4 + - - -
164A GLY 3.1 4.6 + - - -
166A TYR* 1.3 77.6 - - - +
168A ALA* 1.3 60.5 + - - +
170A ALA* 3.1 13.1 + - - +
171A TRP* 3.1 22.4 + - - -
201A GLY* 3.5 19.1 - - - -
204A VAL* 6.0 1.8 - - - -
205A ALA* 4.4 4.7 - - - -
247A LEU* 4.9 7.4 - - - -
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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 GLY 3.0 12.4 + - - +
165A GLU* 3.8 9.4 - - - +
166A TYR 3.3 0.2 - - - -
167A GLY* 1.3 76.1 - - - +
169A GLU* 1.3 63.6 + - - +
171A TRP* 3.3 3.9 + - - +
172A GLU* 3.0 23.8 + - - +
197A VAL* 4.0 9.5 - - + +
198A LYS* 3.8 38.4 - - + +
201A GLY* 3.6 8.6 - - - -
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Residues in contact with GLU 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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165A GLU 3.2 13.8 + - - +
166A TYR* 3.6 8.4 - - - +
167A GLY 3.2 0.4 - - - -
168A ALA* 1.3 77.3 - - - +
170A ALA* 1.3 57.6 + - - +
172A GLU* 3.3 10.5 + - - +
173A ARG* 2.8 69.3 + - + +
250A THR* 3.8 11.9 - - + +
253A ALA* 4.7 0.3 - - - +
254A HIS* 2.8 35.7 + - - -
124D PRO* 4.6 9.4 - - + -
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Residues in contact with ALA 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 TYR 2.9 13.2 + - - +
167A GLY 3.1 8.9 + - - +
169A GLU* 1.3 77.6 - - - +
171A TRP* 1.3 58.2 + - + +
173A ARG* 3.3 4.4 + - - +
174A MET* 3.0 27.7 + - - +
243A LEU* 4.5 7.2 - - + -
246A CYS* 3.6 8.0 - - - +
247A LEU* 3.5 38.4 - - + +
250A THR* 3.5 15.4 + - - +
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Residues in contact with TRP 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 GLY* 3.1 23.3 + - - -
168A ALA* 3.8 6.3 - - - +
170A ALA* 1.3 75.7 - - + +
172A GLU* 1.3 66.1 + - - +
174A MET* 3.0 30.4 + - + +
175A PHE* 2.8 48.3 + + + -
185A PHE* 3.3 23.6 - + - -
197A VAL* 3.9 15.7 - - + -
200A GLN* 3.4 35.6 - - + +
201A GLY* 3.7 14.1 - - - -
204A VAL* 3.5 33.2 - - + +
243A LEU* 3.9 25.9 - - + +
247A LEU* 6.3 0.4 - - + -
285A HEM 3.7 29.8 - + + -
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Residues in contact with GLU 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 3.0 14.0 + - - +
169A GLU* 3.5 13.0 - - - +
171A TRP* 1.3 75.6 - - - +
173A ARG* 1.3 63.7 + - - +
175A PHE* 3.4 8.7 + - - +
176A LEU* 3.2 33.7 + - + +
192A HIS* 2.5 52.2 + - - +
193A GLY 4.9 1.6 + - - -
197A VAL* 4.2 7.9 - - + +
124D PRO* 4.0 25.5 - - + +
125D PRO* 5.5 1.6 - - - +
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Residues in contact with ARG 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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169A GLU* 2.8 46.2 + - - +
170A ALA 3.5 5.2 - - - +
171A TRP 3.2 0.2 - - - -
172A GLU* 1.3 76.6 - - - +
174A MET* 1.3 58.9 + - - +
176A LEU* 3.9 1.7 - - - +
177A SER* 2.9 35.5 + - - -
246A CYS* 4.0 14.1 - - + -
249A VAL* 4.0 15.2 - - - +
250A THR* 3.3 22.8 + - - +
253A ALA* 4.2 13.5 - - - +
119D GLY 5.2 0.6 + - - -
120D LYS* 5.8 1.2 + - - +
122D PHE* 2.9 30.3 + - - -
123D THR* 3.7 11.9 + - - +
124D PRO* 3.9 28.0 - - + +
127D GLN* 3.0 36.9 + - - +
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Residues in contact with MET 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 ALA 3.0 13.2 + - - +
171A TRP* 3.0 46.4 + - + +
173A ARG* 1.3 76.2 - - - +
175A PHE* 1.3 69.9 + - + +
178A PHE* 2.9 38.3 + - + +
181A THR* 3.7 37.7 - - + +
239A ASN 4.4 2.9 - - - +
242A LEU* 4.1 1.3 - - - -
243A LEU* 3.5 37.0 - - + +
246A CYS* 3.5 17.2 - - + -
285A HEM 4.1 7.4 - - + -
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Residues in contact with PHE 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 TRP* 2.8 58.8 + + + +
172A GLU* 4.1 5.4 - - - +
174A MET* 1.3 76.7 - - + +
176A LEU* 1.3 66.7 + - + +
179A PRO* 3.7 19.1 - - - +
181A THR* 3.4 25.1 - - - -
182A LYS* 3.8 34.3 + - + +
185A PHE* 3.6 39.5 - + - -
188A PHE* 5.6 0.9 - + - -
190A LEU* 3.6 30.7 - - + +
197A VAL* 4.2 16.6 - - + -
200A GLN* 5.9 0.9 - - + -
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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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172A GLU* 3.2 27.3 + - + +
173A ARG 3.9 2.9 - - - +
175A PHE* 1.3 83.1 - - + +
177A SER* 1.3 62.0 + - - +
179A PRO* 4.2 9.2 - - - +
190A LEU 6.2 0.4 - - - +
124D PRO* 3.6 29.4 - - + +
125D PRO* 3.7 25.8 - - + -
128D ALA* 3.8 18.6 - - + +
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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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173A ARG 2.9 20.1 + - - -
176A LEU* 1.3 77.5 - - - +
178A PHE* 1.3 83.6 + - - +
179A PRO* 3.5 7.1 - - - +
124D PRO 4.6 0.7 + - - -
127D GLN* 3.5 18.9 - - - +
128D ALA* 3.4 26.8 + - - +
131D GLN* 3.8 22.6 - - - +
132D LYS* 5.8 3.1 - - - +
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Residues in contact with PHE 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 MET* 2.9 15.4 + - + +
175A PHE 4.2 0.2 - - - +
177A SER* 1.3 94.2 - - - +
179A PRO* 1.3 65.8 - - - +
180A THR* 3.1 4.5 - - - +
181A THR* 2.9 29.6 + - + -
242A LEU* 4.0 53.4 - - + -
245A HIS* 4.1 14.4 - + + -
246A CYS* 3.8 24.7 - - - -
108D ASN* 5.4 1.8 - - - -
131D GLN* 3.9 30.5 - - + -
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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
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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