Contacts of the helix formed by residues 175 - 192 (chain A) in PDB entry 1PVS
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 PRO 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A LYS* 5.0 3.6 - - + +
174A MET* 1.3 93.3 - - + +
176A LEU* 1.3 65.5 + - - +
177A LYS* 4.2 13.2 - - + +
178A ARG* 3.2 48.9 + - + +
179A ALA* 3.2 9.5 + - - +
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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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166A PRO* 3.7 33.7 - - + +
167A GLN* 3.6 26.9 - - - +
170A LYS* 4.4 19.0 - - + +
174A MET 3.8 0.4 + - - -
175A PRO* 1.3 72.2 - - - +
177A LYS* 1.3 66.2 + - + +
179A ALA* 3.1 6.5 + - - +
180A GLU* 2.8 47.1 + - - +
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Residues in contact with LYS 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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175A PRO* 3.2 8.9 - - + -
176A LEU* 1.3 79.5 - - + +
178A ARG* 1.3 56.9 + - - +
180A GLU* 2.9 18.1 + - - +
181A ALA* 2.9 29.6 + - - +
213A PRO 5.7 0.3 - - - -
214A GLY* 5.2 11.3 - - - +
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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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121A ILE* 3.5 22.9 - - + -
122A LEU* 4.7 7.9 + - + +
124A GLN* 2.7 65.1 + - - +
125A LEU* 3.4 20.6 + - - +
126A VAL* 5.6 3.2 - - - +
134A LEU* 5.9 1.4 - - - +
174A MET* 3.7 22.0 - - + +
175A PRO* 3.2 46.6 + - + +
177A LYS* 1.3 77.6 - - - +
179A ALA* 1.3 62.8 + - - +
181A ALA* 3.1 9.3 + - - +
182A LEU* 3.1 27.4 + - - +
214A GLY* 6.1 0.9 - - - -
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Residues in contact with ALA 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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166A PRO* 3.4 29.8 - - + +
169A LEU* 3.8 17.4 - - + +
170A LYS 4.2 2.5 - - - +
174A MET* 3.6 12.5 - - - -
175A PRO 3.2 7.5 + - - +
176A LEU* 3.1 10.9 + - - +
178A ARG* 1.3 79.6 - - - +
180A GLU* 1.3 59.4 + - - +
182A LEU* 3.8 6.9 + - - +
183A ILE* 3.1 30.2 + - - +
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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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166A PRO* 4.8 11.5 - - + +
176A LEU* 2.8 45.6 + - + +
177A LYS* 2.9 18.8 + - - +
179A ALA* 1.3 75.7 - - - +
181A ALA* 1.3 66.6 + - - +
182A LEU 3.2 0.4 - - - -
183A ILE* 3.4 9.1 + - + +
184A HIS* 3.0 24.4 + - - +
213A PRO* 5.1 5.4 - - + +
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Residues in contact with ALA 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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121A ILE* 4.1 21.5 - - + +
177A LYS 2.9 11.2 + - - +
178A ARG* 3.3 11.9 - - - +
180A GLU* 1.3 78.2 - - - +
182A LEU* 1.3 57.2 + - - +
184A HIS* 3.2 6.8 + - - +
185A LEU* 2.9 28.1 + - - +
213A PRO* 3.2 27.9 - - - +
214A GLY* 3.9 14.4 - - - +
215A ILE* 5.3 2.2 - - + +
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Residues in contact with LEU 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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114A PHE* 5.2 1.0 - - - -
118A VAL* 4.1 28.6 - - + +
121A ILE* 3.5 37.5 - - + -
122A LEU* 4.0 9.2 - - + -
138A VAL* 5.6 2.7 - - + -
161A LEU* 4.9 12.8 - - + +
169A LEU* 4.2 19.5 - - + -
174A MET* 3.6 37.2 - - + -
178A ARG 3.2 9.2 - - - +
179A ALA 3.9 4.7 - - - +
180A GLU 3.2 0.2 - - - -
181A ALA* 1.3 78.0 - - - +
183A ILE* 1.3 57.0 + - - +
185A LEU* 3.1 8.5 + - - +
186A ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 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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161A LEU 3.8 16.2 - - - +
162A ALA 3.8 19.3 - - - +
164A ALA 3.4 17.7 - - - +
166A PRO* 3.4 37.7 - - + -
169A LEU* 4.3 9.2 - - + -
179A ALA 3.1 20.1 + - - +
180A GLU* 3.7 8.3 - - + +
181A ALA 3.3 0.2 - - - -
182A LEU* 1.3 76.4 - - - +
184A HIS* 1.3 63.1 + - - +
186A ALA* 3.3 5.5 + - - +
187A ASN* 3.3 26.6 + - - +
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Residues in contact with HIS 184 (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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180A GLU 3.0 17.9 + - - +
181A ALA 3.6 4.7 - - - +
183A ILE* 1.3 74.5 - - - +
185A LEU* 1.3 67.4 + - + +
187A ASN* 3.1 11.6 + - + +
188A ALA* 2.9 24.0 + - + +
212A PHE* 3.2 49.1 - + + -
213A PRO* 3.4 34.0 - - + +
215A ILE* 5.8 0.4 - - + -
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Residues in contact with LEU 185 (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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114A PHE* 4.0 12.6 - - + +
117A GLY* 3.7 11.7 - - - +
118A VAL* 3.6 45.8 - - + +
121A ILE* 4.1 9.9 - - + -
181A ALA 2.9 14.1 + - - +
182A LEU* 3.3 9.4 - - - +
184A HIS* 1.3 79.3 - - - +
186A ALA* 1.3 56.5 + - - +
188A ALA* 3.2 6.3 + - - +
189A ALA* 2.9 29.1 + - - +
194A LEU* 3.9 31.6 - - + -
209A LEU* 5.4 0.4 - - + -
212A PHE* 5.1 5.2 - - + -
215A ILE* 4.7 19.3 - - + -
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Residues in contact with ALA 186 (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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114A PHE* 3.8 13.5 - - + -
158A PRO* 3.5 24.5 - - + +
161A LEU* 3.8 23.1 - - + +
162A ALA* 3.8 2.5 - - - +
182A LEU 2.9 11.7 + - - +
183A ILE 3.3 11.2 - - - +
185A LEU* 1.3 78.6 - - - +
187A ASN* 1.3 56.9 + - - +
189A ALA* 3.4 4.7 + - - +
190A LEU* 3.1 31.2 + - - +
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Residues in contact with ASN 187 (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* 4.2 17.0 - - - +
183A ILE* 3.3 17.2 + - - +
184A HIS* 3.1 14.0 + - + +
186A ALA* 1.3 78.0 - - - +
188A ALA* 1.3 65.0 + - - +
190A LEU* 3.3 23.4 + - - +
191A GLU* 3.1 36.0 + - - +
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Residues in contact with ALA 188 (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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184A HIS* 2.9 17.4 + - + +
185A LEU* 3.2 10.1 + - + +
187A ASN* 1.3 77.1 - - - +
189A ALA* 1.3 57.3 + - - +
191A GLU* 3.4 3.0 + - - -
192A GLY 2.9 25.1 + - - -
193A THR* 3.0 31.6 + - - +
194A LEU* 3.7 10.4 + - + -
212A PHE* 3.6 25.1 - - + -
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Residues in contact with ALA 189 (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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114A PHE* 3.8 29.2 - - + -
158A PRO* 4.1 12.8 - - + -
185A LEU 2.9 13.2 + - - +
186A ALA 3.5 9.2 - - - +
188A ALA* 1.3 78.0 - - - +
190A LEU* 1.3 61.6 + - - +
192A GLY* 3.3 13.0 + - - +
194A LEU* 4.4 14.3 - - + +
196A MET* 5.3 7.6 - - - +
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Residues in contact with LEU 190 (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 PRO* 3.7 9.6 - - + +
159A GLN* 3.6 40.2 - - + +
162A ALA* 4.0 17.3 - - + -
186A ALA 3.1 14.0 + - - +
187A ASN* 3.5 30.5 - - - +
188A ALA 3.3 0.2 - - - -
189A ALA* 1.3 79.1 - - - +
191A GLU* 1.3 61.2 + - + +
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Residues in contact with GLU 191 (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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187A ASN* 3.1 26.2 + - - +
188A ALA* 4.0 3.6 - - - +
190A LEU* 1.3 78.5 - - + +
192A GLY* 1.3 60.3 + - - +
193A THR* 4.1 20.8 - - + +
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Residues in contact with GLY 192 (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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188A ALA 2.9 6.0 + - - -
189A ALA 3.3 10.3 + - - -
191A GLU* 1.3 79.9 - - - +
193A THR* 1.3 63.1 + - - +
194A LEU 3.3 10.2 - - - +
195A PRO* 5.6 0.3 - - - +
196A MET* 6.4 0.9 - - - -
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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