Contacts of the helix formed by residues 171 - 183 (chain A) in PDB entry 1PJQ
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 THR 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ALA* 1.3 79.7 - - + +
172A MET* 1.3 65.7 + - - +
173A GLY 3.8 2.4 + - - -
174A GLU* 2.5 55.1 + - - +
175A ARG* 3.2 16.4 - - - +
214A HIS* 3.2 35.5 - - + +
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Residues in contact with MET 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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171A THR* 1.3 75.1 - - - +
173A GLY* 1.3 61.0 + - - +
175A ARG* 3.3 11.0 + - - +
176A ARG* 2.8 37.3 + - + +
243A ASP* 3.3 40.6 - - + +
292A LYS 4.9 4.7 - - - +
293A GLY* 4.0 25.1 - - - +
294A LYS* 4.4 10.8 - - + -
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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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171A THR* 3.3 6.4 + - - -
172A MET* 1.3 85.2 - - - +
174A GLU* 1.3 56.1 + - - +
176A ARG* 3.6 24.1 + - - +
177A ARG* 3.0 36.1 + - - +
213A ASP 3.8 6.3 - - - -
214A HIS 4.4 11.1 + - - -
215A ARG 5.1 0.4 - - - -
293A GLY 4.7 2.5 - - - -
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Residues in contact with GLU 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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169A PHE* 3.6 31.5 - - + -
170A ALA* 3.6 6.4 + - - +
171A THR* 2.5 53.5 + - - +
173A GLY* 1.3 72.5 - - - +
175A ARG* 1.3 61.8 + - - +
176A ARG 3.2 1.1 - - - -
177A ARG* 4.0 4.0 - - - -
178A PHE* 2.8 25.8 + - - +
212A LEU* 3.2 38.0 + - + +
213A ASP 3.8 7.6 + - - +
214A HIS* 4.0 8.8 - - - +
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Residues in contact with ARG 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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165A VAL* 4.3 16.8 - - + -
166A LYS* 3.2 54.0 + - - +
169A PHE* 2.9 34.4 + - + +
170A ALA* 3.1 25.5 + - - +
171A THR 3.2 12.3 - - - +
172A MET* 3.3 9.7 + - - +
174A GLU* 1.3 77.1 - - - +
176A ARG* 1.3 61.1 + - - +
178A PHE* 3.4 8.3 + - - +
179A TRP* 2.9 36.4 + - - +
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Residues in contact with ARG 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 MET* 2.8 19.3 + - + +
173A GLY* 3.6 25.5 + - - +
175A ARG* 1.3 78.4 - - - +
177A ARG* 1.3 72.4 + - - +
179A TRP* 3.5 9.5 + - - +
180A GLU* 3.2 38.4 + - + +
215A ARG 4.6 8.5 + - - -
216A GLY* 5.1 2.2 - - - -
217A GLU* 4.6 6.1 + - - -
241A GLN* 4.9 6.1 - - - -
243A ASP* 4.5 13.0 + - - +
293A GLY 4.3 11.5 + - - -
295A ARG* 3.0 64.7 - - - +
134B VAL* 6.2 4.5 - - + -
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Residues in contact with ARG 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 GLY* 3.0 23.7 + - - +
174A GLU* 3.3 6.5 + - - +
176A ARG* 1.3 90.2 - - - +
178A PHE* 1.3 66.1 + - - +
180A GLU* 3.4 16.1 + - - +
181A LYS* 3.2 28.3 + - - +
212A LEU* 4.2 14.1 - - + +
213A ASP* 2.6 69.5 + - - +
214A HIS 3.7 0.8 - - - +
215A ARG* 3.1 26.6 + - - +
216A GLY 4.9 2.8 + - - -
217A GLU* 4.2 17.2 + - - -
323A PRO* 5.6 4.4 - - - +
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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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161A LEU* 4.6 4.0 - - + -
165A VAL* 3.5 21.3 - - + -
169A PHE* 3.9 19.5 - + + -
174A GLU 2.8 16.5 + - - +
175A ARG* 3.4 9.9 - - - +
176A ARG 3.2 0.2 - - - -
177A ARG* 1.3 76.5 - - - +
179A TRP* 1.3 88.4 + + - +
181A LYS* 2.9 8.4 + - - +
182A PHE* 2.8 39.6 + + + +
207A LEU* 3.6 48.6 - - + +
208A PHE* 3.8 34.8 - + - -
212A LEU* 3.8 9.6 - - + +
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Residues in contact with TRP 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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158A ALA* 3.5 39.7 - - + -
161A LEU* 4.5 2.9 - - + -
162A ARG* 4.4 19.5 - - + -
165A VAL* 3.8 34.4 - - + +
175A ARG* 2.9 26.9 + - - +
176A ARG* 3.9 8.5 - - - +
177A ARG 3.5 0.2 - - - -
178A PHE* 1.3 96.2 - + - +
180A GLU* 1.3 57.1 + - - +
182A PHE* 3.8 12.6 - + - -
183A PHE* 2.9 61.4 + + + -
132B SER* 5.6 1.1 - - - -
134B VAL* 4.0 30.8 - - + +
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Residues in contact with GLU 180 (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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176A ARG* 3.2 27.5 + - + +
177A ARG* 3.7 20.1 - - - +
178A PHE 3.2 0.8 - - - -
179A TRP* 1.3 78.4 - - + +
181A LYS* 1.3 64.3 + - + +
183A PHE* 4.0 1.8 + - - +
184A VAL* 3.3 28.8 + - - +
241A GLN* 3.4 12.4 + - - +
295A ARG* 2.7 37.9 + - - -
134B VAL* 6.1 3.4 - - + -
138B LEU* 6.5 0.4 - - - -
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Residues in contact with LYS 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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177A ARG* 3.2 14.8 + - - +
178A PHE* 2.9 8.9 + - - +
180A GLU* 1.3 75.9 - - + +
182A PHE* 1.3 66.5 + - - +
184A VAL* 3.3 6.9 + - - +
185A ASN* 3.2 25.6 + - - +
207A LEU* 4.1 18.8 - - + -
210A GLU* 2.7 32.4 + - - +
211A PRO 5.7 0.2 + - - -
212A LEU* 3.6 22.9 - - + +
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Residues in contact with PHE 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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154A VAL* 3.7 27.8 - - + +
157A TYR* 3.7 19.5 - + - -
158A ALA* 3.9 27.6 - - + -
161A LEU* 3.7 22.0 - - + -
178A PHE* 2.8 24.5 + + + +
179A TRP* 3.2 21.1 + + + +
181A LYS* 1.3 77.0 - - - +
183A PHE* 1.3 77.9 + + - +
184A VAL 3.1 4.3 + - - -
185A ASN* 3.3 19.1 + - - +
188A LEU* 3.4 30.9 - - + +
204A THR* 5.7 0.2 - - - -
207A LEU* 4.0 19.2 - - + +
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Residues in contact with PHE 183 (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 LEU* 6.4 0.9 - - + -
154A VAL* 4.0 18.6 - - + -
158A ALA* 4.0 11.0 - - + -
179A TRP* 2.9 47.1 + + + +
180A GLU* 4.8 2.2 - - - +
182A PHE* 1.3 95.9 - + - +
184A VAL* 1.3 60.9 + - + +
185A ASN 3.5 1.5 - - - +
132B SER* 3.0 29.4 - - - -
134B VAL* 3.7 23.3 - - + -
135B LEU* 3.6 30.5 - - + -
138B LEU* 4.0 19.3 - - + -
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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