Contacts of the helix formed by residues 196 - 213 (chain A) in PDB entry 1P4F
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 LEU 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A HIS* 3.3 67.3 - - + +
134A GLN* 3.8 35.9 - - - +
135A ILE 3.9 3.8 - - - +
136A ALA* 3.8 25.6 - - + +
168A ILE* 4.3 9.0 - - + -
171A GLY 5.0 1.0 + - - +
195A GLY* 1.3 72.1 - - - -
197A GLU* 1.3 66.8 + - + +
199A ASP* 3.1 12.9 + - - +
200A MET* 3.6 3.1 + - - +
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Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLY 4.8 5.1 - - - +
187A GLU* 4.3 1.2 - - - +
195A GLY* 3.4 21.5 + - - -
196A LEU* 1.3 81.4 - - - +
198A ALA* 1.3 62.0 + - - +
200A MET* 3.0 22.4 + - - +
201A TRP 3.2 5.2 + - - -
260A PRO* 3.4 40.2 - - + +
261A LYS* 5.6 3.1 - - - +
263A ARG* 2.8 29.0 + - + +
264A MET 5.8 0.9 - - - +
265A THR* 6.1 5.6 - - + -
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PHE* 3.9 19.5 - - + -
185A ALA* 4.0 12.6 + - + +
187A GLU* 3.5 23.3 + - + +
188A ILE* 4.3 13.9 - - + -
194A LEU* 5.2 0.9 - - + -
195A GLY 3.2 15.2 + - - +
196A LEU 3.2 0.6 - - - -
197A GLU* 1.3 77.5 - - - +
199A ASP* 1.3 62.4 + - - +
200A MET 3.3 0.2 + - - -
201A TRP* 3.3 5.0 + - - +
202A SER* 3.2 23.5 + - - -
263A ARG* 3.8 2.2 - - - +
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Residues in contact with ASP 199 (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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127A VAL* 4.7 2.0 - - + +
130A LEU* 5.6 0.5 - - - +
131A HIS* 2.9 35.7 + - + +
136A ALA* 3.3 6.9 - - - -
137A HIS* 2.8 26.1 + - - +
138A PHE* 2.9 30.0 + - - -
140A LEU* 3.8 23.5 + - + +
195A GLY 4.4 0.2 + - - -
196A LEU 3.1 5.1 + - - +
198A ALA* 1.3 78.3 - - - +
200A MET* 1.3 59.2 + - - +
202A SER* 3.2 7.6 + - - -
203A ILE* 2.9 31.4 + - - +
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Residues in contact with MET 200 (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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124A LEU* 4.9 0.2 - - + -
131A HIS* 3.9 11.7 - - + -
196A LEU 4.0 11.2 - - - +
197A GLU* 3.0 12.4 + - - +
199A ASP* 1.3 74.3 - - - +
201A TRP* 1.3 66.9 + - - +
203A ILE* 3.2 26.4 + - + +
204A GLY 3.1 16.6 + - - -
255A LEU* 3.8 29.8 - - + +
263A ARG* 4.3 3.6 - - - -
264A MET 3.5 20.2 - - - +
265A THR* 3.7 8.5 - - - +
266A ILE* 3.6 52.7 - - + +
269A SER* 3.9 8.3 - - - +
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Residues in contact with TRP 201 (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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182A GLU 5.3 0.2 + - - -
183A PHE 3.8 6.5 - - - -
184A VAL 3.3 14.0 + - - -
185A ALA* 3.5 22.2 - - + -
186A PRO* 3.5 38.1 - - + -
197A GLU 3.2 4.6 + - - -
198A ALA 3.3 8.5 + - - +
200A MET* 1.3 77.3 - - - +
202A SER* 1.3 65.5 + - - +
204A GLY* 2.9 13.7 + - - +
205A VAL* 3.0 26.9 + - + +
217A PHE* 3.3 36.6 - + - -
229A VAL* 4.0 16.3 - - + +
232A VAL* 4.2 8.1 - - + -
255A LEU 3.8 20.2 - - - -
256A LEU* 3.5 31.8 - - + +
257A VAL 3.6 18.6 - - - -
258A LYS 4.3 0.9 - - - -
263A ARG* 3.7 11.3 - - - +
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Residues in contact with SER 202 (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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138A PHE 5.8 2.3 - - - -
140A LEU* 3.6 35.0 + - - +
183A PHE* 2.8 25.9 + - - -
184A VAL* 4.7 2.1 - - - -
185A ALA 5.0 0.2 + - - -
198A ALA 3.2 11.2 + - - -
199A ASP* 3.2 12.1 + - - -
201A TRP* 1.3 79.2 - - - +
203A ILE* 1.3 56.4 + - - +
205A VAL* 3.2 5.7 + - - +
206A ILE* 2.9 33.6 + - - +
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Residues in contact with ILE 203 (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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120A LEU* 4.1 15.7 - - + -
123A ILE* 4.6 11.7 - - + -
124A LEU* 3.9 27.8 - - + -
127A VAL* 4.0 29.2 - - + -
140A LEU* 4.2 10.3 - - + -
199A ASP 2.9 19.1 + - - +
200A MET* 3.5 33.7 - - + +
202A SER* 1.3 75.9 - - - +
204A GLY* 1.3 55.9 + - - +
206A ILE* 3.3 10.2 + - + +
207A THR* 2.9 35.6 + - - +
251A PHE* 4.7 0.9 - - + -
255A LEU* 4.1 13.2 - - + -
266A ILE* 4.3 0.2 - - + -
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Residues in contact with GLY 204 (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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200A MET 3.1 7.5 + - - -
201A TRP 2.9 9.4 + - - -
203A ILE* 1.3 74.8 - - - +
205A VAL* 1.3 56.7 + - - +
207A THR* 3.3 5.3 + - - -
208A TYR* 2.9 29.8 + - - +
252A ILE* 4.0 7.9 - - - +
255A LEU* 3.6 28.7 - - - +
256A LEU* 3.9 12.1 - - - -
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Residues in contact with VAL 205 (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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182A GLU 3.6 16.6 - - - +
183A PHE* 3.5 33.4 - - + -
201A TRP* 3.0 38.6 + - + +
202A SER* 3.2 8.9 + - - +
204A GLY* 1.3 77.1 - - - +
206A ILE* 1.3 61.9 + - - +
208A TYR* 3.2 3.2 + - - +
209A ILE* 3.1 22.9 + - + +
215A SER* 5.0 0.7 - - - +
216A PRO* 3.9 23.1 - - + -
217A PHE* 4.3 9.0 - - + -
256A LEU* 3.7 8.0 - - + +
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Residues in contact with ILE 206 (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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102A PHE* 3.8 19.1 - - + -
120A LEU* 5.2 2.7 - - + -
123A ILE* 4.3 23.6 - - + -
140A LEU* 3.9 13.5 - - + -
141A LYS* 3.7 28.9 - - - +
142A PRO* 4.0 20.4 - - + -
145A ILE* 4.6 13.2 - - + -
183A PHE* 4.8 3.1 - - + -
202A SER 2.9 20.3 + - - +
203A ILE* 3.6 12.8 - - + +
205A VAL* 1.3 73.9 - - - +
207A THR* 1.3 54.0 + - - +
209A ILE* 3.3 7.8 + - - -
210A LEU* 2.8 40.6 + - + +
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Residues in contact with THR 207 (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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120A LEU* 3.4 25.1 - - + +
203A ILE 2.9 20.7 + - - -
204A GLY* 3.6 6.5 - - - -
206A ILE* 1.3 70.6 - - - +
208A TYR* 1.3 65.7 + - - +
210A LEU* 3.3 10.2 + - + +
211A LEU* 3.1 27.1 + - + +
251A PHE* 3.8 10.0 - - + -
252A ILE* 3.7 22.7 - - + -
274A TRP* 3.9 32.3 - - + -
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Residues in contact with TYR 208 (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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204A GLY 2.9 13.9 + - - +
205A VAL 3.4 8.7 - - - +
207A THR* 1.3 76.2 - - - +
209A ILE* 1.3 55.1 + - - +
211A LEU* 3.4 1.0 + - - -
212A SER* 2.8 41.6 + - - -
214A ALA* 3.2 29.8 - - + +
215A SER 4.1 0.8 + - - -
216A PRO* 3.5 38.9 - - + +
234A TYR* 3.8 19.5 - + - -
235A GLU 2.6 28.9 + - - -
236A PHE* 3.9 16.2 - + - -
237A GLU* 4.1 7.4 + - - +
240A TYR* 5.4 0.5 - - - -
241A PHE* 3.5 29.4 - + - -
252A ILE* 3.8 17.6 - - + +
256A LEU* 4.8 0.2 - - + -
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Residues in contact with ILE 209 (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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102A PHE* 3.2 28.0 - - + -
142A PRO* 4.5 6.7 - - + -
182A GLU* 4.7 0.4 - - - +
183A PHE* 3.4 36.3 - - + -
205A VAL* 3.1 20.1 + - + +
206A ILE* 3.8 2.7 - - - +
208A TYR* 1.3 70.9 - - - +
210A LEU* 1.3 62.9 + - - +
212A SER* 4.1 0.2 - - - -
213A GLY* 2.7 39.3 + - - +
214A ALA 3.2 23.1 - - - +
215A SER* 3.9 18.4 - - - +
216A PRO* 4.1 1.8 - - + -
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Residues in contact with LEU 210 (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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101A LEU* 4.0 17.9 - - + -
102A PHE* 3.4 29.8 - - + -
116A ALA* 3.9 40.7 - - + +
119A PHE* 5.2 3.8 - - + -
120A LEU* 4.4 18.8 - - + +
123A ILE* 5.2 1.3 - - + -
206A ILE* 2.8 33.2 + - + +
207A THR* 3.4 12.6 - - + +
209A ILE* 1.3 72.7 - - - +
211A LEU* 1.3 63.6 + - + +
212A SER 3.8 0.2 + - - -
213A GLY 4.7 0.5 + - - -
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Residues in contact with LEU 211 (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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112A THR 4.9 1.3 - - - +
113A GLU* 4.0 22.4 - - + +
116A ALA* 3.5 30.7 - - + -
207A THR* 3.1 21.6 + - + +
208A TYR 4.0 2.9 - - - +
209A ILE 3.1 0.2 - - - -
210A LEU* 1.3 77.0 - - + +
212A SER* 1.3 58.5 + - - +
240A TYR 4.5 5.7 - - - +
241A PHE* 4.4 9.6 - - + -
243A ASN* 6.0 0.3 + - - -
244A THR* 4.0 18.1 + - + +
248A ALA* 3.7 29.2 - - + -
252A ILE* 3.9 17.5 - - + -
274A TRP* 3.9 15.0 - - + -
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Residues in contact with SER 212 (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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208A TYR* 2.8 23.2 + - - -
211A LEU* 1.3 79.6 - - - +
213A GLY* 1.3 60.2 + - - +
214A ALA* 3.0 26.1 + - - +
240A TYR* 4.0 28.3 - - - +
241A PHE* 3.6 26.7 - - - -
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Residues in contact with GLY 213 (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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209A ILE* 2.7 29.8 + - - +
210A LEU 4.7 0.6 + - - -
211A LEU 3.9 0.4 - - - -
212A SER* 1.3 70.7 - - - +
214A ALA* 1.3 56.9 + - - +
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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