Contacts of the helix formed by residues 165 - 176 (chain A) in PDB entry 5JQE
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 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ASN* 4.0 11.7 + - - +
163A LEU 4.4 1.3 - - - -
164A GLN* 1.3 95.4 - - + +
166A PRO* 1.3 82.8 - - + +
167A TYR* 3.3 6.4 + - + +
168A PHE* 3.4 30.5 + - + +
169A THR* 3.4 15.9 + - - +
352A TRP* 5.8 0.9 - - - +
356A ARG* 3.5 27.1 + - - -
359A VAL* 5.5 2.5 - - - -
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Residues in contact with PRO 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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165A GLU* 1.3 93.0 - - + +
167A TYR* 1.3 60.4 + - - +
168A PHE 3.0 2.7 - - - -
169A THR* 3.3 10.8 - - - +
170A TRP* 2.6 41.6 + - + +
351A PHE* 5.6 0.9 - - + -
352A TRP* 4.0 27.6 - - + +
355A VAL* 3.7 22.7 - - + -
356A ARG* 3.5 40.2 - - + +
359A VAL* 5.3 1.6 - - + -
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 4.8 4.7 + - - +
124A ALA* 4.4 7.4 - - - -
125A LEU* 3.4 37.7 - - + +
165A GLU* 3.3 4.8 - - + -
166A PRO* 1.3 79.3 - - - +
168A PHE* 1.3 81.6 + + + +
170A TRP* 4.6 0.9 - - - +
171A PRO* 3.6 12.1 - - - +
242A TRP* 3.8 30.7 - + - -
270A PHE* 3.6 50.2 + + + -
272A GLY 5.4 1.4 + - - -
342A MET* 4.4 11.7 - - + -
352A TRP* 4.0 20.3 - + + -
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Residues in contact with PHE 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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125A LEU* 3.8 19.0 - - + +
161A PHE* 3.4 18.8 - + + -
162A ASN* 3.1 50.9 - - + +
165A GLU* 3.4 16.6 + - + +
166A PRO 3.0 0.6 - - - -
167A TYR* 1.3 98.5 - + + +
169A THR* 1.3 59.4 + - - +
170A TRP 3.5 0.2 - - - -
171A PRO* 3.5 12.3 - - - +
172A LEU 5.5 0.3 + - - -
222A TYR* 3.6 35.7 - + - -
238A ILE* 3.8 27.6 - - - +
239A ASN* 4.2 7.6 - - - -
242A TRP* 4.5 10.1 - + - -
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Residues in contact with THR 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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161A PHE* 4.2 4.7 - - + -
162A ASN 4.1 1.6 - - - +
163A LEU* 3.9 40.4 - - + +
165A GLU 3.4 5.3 + - - +
166A PRO* 3.0 20.6 + - - +
168A PHE* 1.3 77.7 - - - +
170A TRP* 1.3 63.3 + - - +
171A PRO* 3.4 2.0 - - - -
172A LEU* 3.7 7.5 + - - +
173A ILE* 3.3 26.0 + - - +
207A LEU* 3.9 28.1 - - + +
359A VAL* 4.2 16.3 - - + +
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Residues in contact with TRP 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 PRO* 2.6 22.6 + - + +
169A THR* 1.3 71.6 + - - +
171A PRO* 1.3 64.1 - - + +
173A ILE* 3.8 25.6 - - + -
174A ALA* 2.7 43.8 + - + +
178A GLY* 4.0 4.0 - - - -
179A TYR 3.7 31.9 - - - -
180A ALA 3.9 0.2 - - - -
195A VAL* 4.1 22.7 - - + -
200A ALA* 5.5 0.2 - - + -
268A LYS 4.1 8.5 - - - -
270A PHE* 3.2 37.6 - + + -
340A GLU* 3.2 21.2 + - - -
351A PHE* 3.6 36.6 - + - -
355A VAL* 4.0 24.7 - - + -
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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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125A LEU* 4.5 6.1 - - + -
141A TRP* 6.1 2.5 - - + -
167A TYR 3.6 12.6 - - - +
168A PHE 3.5 15.3 - - - +
169A THR 3.4 4.5 - - - -
170A TRP* 1.3 93.9 - - + +
172A LEU* 1.3 60.4 + - - +
174A ALA 4.1 0.2 - - - -
175A ALA* 3.3 18.4 + - - +
238A ILE* 5.5 4.3 - - + -
259A LEU* 4.1 22.0 - - + -
267A SER* 3.7 7.4 - - - -
268A LYS 3.3 31.5 + - - +
269A PRO* 3.8 22.0 - - + -
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Residues in contact with LEU 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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141A TRP* 3.8 47.0 - - + +
161A PHE* 5.9 1.6 - - + -
168A PHE 5.5 0.2 + - - -
169A THR* 3.7 8.8 + - - +
170A TRP 3.3 0.4 - - - -
171A PRO* 1.3 77.3 - - - +
173A ILE* 1.3 64.9 + - + +
175A ALA* 3.5 14.0 + - - +
203A GLY* 3.5 28.9 - - - +
206A PHE* 4.2 11.0 - - + -
207A LEU* 3.7 34.3 - - + +
210A LEU* 5.2 0.4 - - + -
262A PHE* 3.7 35.5 - - + -
267A SER* 4.8 0.8 - - - -
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Residues in contact with ILE 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 THR* 3.3 24.0 + - - +
170A TRP* 3.0 33.5 + - + +
172A LEU* 1.3 80.5 - - + +
174A ALA* 1.3 62.3 + - - +
175A ALA 3.3 0.9 + - - -
176A ASP 4.2 0.3 + - - -
199A GLY 3.3 21.1 - - - +
200A ALA* 3.5 29.0 - - + +
203A GLY* 4.1 6.5 - - - +
204A LEU* 3.7 31.6 - - + +
207A LEU* 4.9 2.7 - - + -
355A VAL* 5.2 0.9 - - + -
359A VAL* 3.7 30.5 - - + -
373A LEU* 5.5 1.6 - - + -
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Residues in contact with ALA 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 TRP* 2.7 45.9 + - + +
171A PRO 4.1 0.4 - - - +
173A ILE* 1.3 72.6 - - - +
175A ALA* 1.3 64.5 + - - +
176A ASP 3.4 0.7 - - - -
177A GLY* 3.2 11.1 + - - -
178A GLY* 3.2 31.1 + - - +
268A LYS* 4.2 22.3 - - + +
340A GLU* 4.1 5.4 - - - +
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Residues in contact with ALA 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 3.3 17.6 + - - +
172A LEU* 3.6 10.3 - - - +
173A ILE 3.2 2.0 - - - -
174A ALA* 1.3 79.2 - - - +
176A ASP* 1.3 58.9 + - - +
177A GLY 3.2 4.0 + - - -
262A PHE* 4.1 22.2 - - + +
265A GLN* 3.4 23.6 - - - +
266A PRO 3.7 23.3 - - - +
267A SER* 4.0 5.6 - - - +
268A LYS* 4.6 5.4 - - - +
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Residues in contact with ASP 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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173A ILE 4.2 2.6 + - - -
174A ALA 3.4 0.6 - - - -
175A ALA* 1.3 76.2 - - - +
177A GLY* 1.3 56.1 + - - +
198A ALA* 3.9 2.4 - - - +
199A GLY* 3.3 30.0 + - - +
202A ALA* 3.2 21.3 - - - +
262A PHE* 3.9 17.8 - - + -
263A LYS* 3.3 23.9 + - - +
265A GLN* 2.5 37.1 + - - +
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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