Contacts of the helix formed by residues 184 - 203 (chain A) in PDB entry 1PH3
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 ASN 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TYR 4.8 11.1 + - - -
37A GLU* 5.7 2.2 + - - -
38A TYR* 5.3 2.2 - - - -
182A GLU* 3.0 26.0 - - - +
183A LYS* 1.3 78.6 - - - +
185A GLU* 1.3 64.1 + - - +
187A SER* 3.2 21.8 + - - -
188A ILE* 3.9 14.9 - - - +
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Residues in contact with GLU 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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38A TYR* 3.3 29.0 + - + -
55A TYR* 2.7 26.5 + - + +
121A ARG* 2.7 30.1 + - - -
180A THR 3.7 1.0 - - - +
181A ILE* 3.2 15.0 - - + +
182A GLU* 2.6 42.4 + - + +
184A ASN* 1.3 84.6 - - - +
186A ILE* 1.3 66.8 + - - +
187A SER 3.1 3.1 - - - -
188A ILE* 2.7 22.8 + - - +
189A LEU* 2.9 12.5 + - + +
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Residues in contact with ILE 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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169A THR* 4.2 28.7 - - + +
181A ILE* 4.8 6.9 - - + +
182A GLU 4.1 6.7 - - - +
183A LYS* 3.3 42.1 + - + +
185A GLU* 1.3 76.4 - - - +
187A SER* 1.3 57.6 + - - +
189A LEU* 3.7 6.7 - - - +
190A GLN* 2.9 64.4 + - + +
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Residues in contact with SER 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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183A LYS 4.5 0.2 + - - -
184A ASN 3.2 15.3 + - - -
185A GLU 3.1 0.2 - - - -
186A ILE* 1.3 79.4 - - - +
188A ILE* 1.3 69.9 + - - +
190A GLN* 4.0 8.9 - - - +
191A ASN* 2.9 46.8 + - - +
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Residues in contact with ILE 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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38A TYR* 4.0 32.5 - - + -
55A TYR* 3.9 33.0 - - + -
184A ASN* 3.9 20.6 - - - +
185A GLU* 2.7 19.5 + - - +
187A SER* 1.3 81.5 + - - +
189A LEU* 1.3 56.6 + - - +
191A ASN* 3.9 4.2 - - - +
192A LEU* 2.9 30.7 + - + +
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Residues in contact with LEU 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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55A TYR* 4.3 21.7 - - + +
119A ILE* 4.1 16.4 - - + -
149A PHE* 3.7 49.4 - - + -
168A ASP 3.5 23.6 - - - +
169A THR* 4.0 12.8 - - + -
181A ILE* 5.9 3.6 - - + -
185A GLU* 2.9 11.7 + - + +
186A ILE* 3.7 8.1 - - - +
188A ILE* 1.3 75.1 - - - +
190A GLN* 1.3 67.3 + - + +
192A LEU* 3.3 3.8 + - - +
193A ARG* 3.0 37.7 + - - +
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Residues in contact with GLN 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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168A ASP* 5.9 5.3 - - + +
169A THR* 5.6 4.0 - - + +
186A ILE* 2.9 52.3 + - + +
187A SER* 4.0 7.5 - - - +
189A LEU* 1.3 73.4 - - + +
191A ASN* 1.3 64.9 + - - +
193A ARG* 3.4 18.3 + - - +
194A LYS* 3.1 20.8 + - - +
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Residues in contact with ASN 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 SER* 2.9 33.0 + - - +
188A ILE* 3.9 4.8 - - - +
190A GLN* 1.3 77.4 - - - +
192A LEU* 1.3 60.3 + - - +
194A LYS* 3.1 13.3 + - - +
195A TRP* 2.9 28.3 + - - +
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Residues in contact with LEU 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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55A TYR* 3.9 15.5 - - + +
56A ALA* 3.8 21.8 - - - +
57A VAL* 3.8 15.5 - - + +
80A ASP* 4.9 5.6 - - + -
81A PRO* 4.3 18.2 - - + -
119A ILE* 3.6 40.8 - - + -
188A ILE* 2.9 20.1 + - + +
189A LEU* 3.3 4.2 + - - +
191A ASN* 1.3 76.3 - - - +
193A ARG* 1.3 56.4 + - - +
195A TRP* 3.5 15.9 + - + -
196A ALA* 2.8 27.4 + - - +
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Residues in contact with ARG 193 (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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119A ILE* 3.8 17.0 - - + +
149A PHE* 4.4 6.9 - - - +
150A SER* 2.8 36.9 + - - +
151A THR* 4.1 20.3 + - - +
152A ASP 5.7 0.4 - - - -
167A SER 5.4 0.4 + - - -
168A ASP* 2.6 50.1 + - - +
170A THR 5.5 2.6 + - - -
189A LEU* 3.0 33.9 + - + +
190A GLN* 3.5 20.1 - - - +
191A ASN 3.1 0.2 - - - -
192A LEU* 1.3 75.8 - - - +
194A LYS* 1.3 66.3 + - - +
196A ALA* 3.2 5.9 + - - +
197A ASN* 3.1 30.9 + - - +
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Residues in contact with LYS 194 (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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190A GLN 3.1 9.6 + - - +
191A ASN* 3.1 16.2 + - - +
193A ARG* 1.3 79.2 - - - +
195A TRP* 1.3 62.8 + - - +
197A ASN* 3.3 9.3 + - - +
198A GLN* 3.1 52.1 + - + +
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Residues in contact with TRP 195 (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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57A VAL* 3.7 27.1 - - + -
79A VAL* 3.7 17.5 - - + -
80A ASP* 3.7 24.9 - - - -
81A PRO* 3.6 33.4 - - + +
84A TYR* 3.9 23.3 - + + -
191A ASN 2.9 15.7 + - - +
192A LEU* 3.6 13.7 - - + +
194A LYS* 1.3 75.1 - - - +
196A ALA* 1.3 70.2 + - - +
198A GLN* 3.0 20.2 + - + +
199A TYR* 2.8 69.5 + + + +
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Residues in contact with ALA 196 (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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57A VAL* 4.0 18.6 - - + -
117A GLY 4.1 15.9 - - - +
119A ILE* 5.0 0.9 - - + -
151A THR* 4.1 11.2 - - + +
192A LEU 2.8 18.9 + - - +
193A ARG* 3.2 7.6 + - - +
195A TRP* 1.3 86.7 - - - +
197A ASN* 1.3 57.9 + - - +
199A TYR* 4.3 0.4 - - - -
200A PHE* 3.0 37.6 + - + +
300A ILE* 4.2 2.6 - - + +
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Residues in contact with ASN 197 (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 THR* 3.9 24.6 + - - +
152A ASP* 4.4 7.5 + - - +
193A ARG* 3.1 23.8 + - - +
194A LYS* 3.8 8.1 - - - +
196A ALA* 1.3 75.2 - - - +
198A GLN* 1.3 62.1 + - + +
201A SER* 2.8 30.5 + - - -
300A ILE* 4.0 1.6 - - - +
302A SER* 2.8 32.7 + - - +
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Residues in contact with GLN 198 (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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194A LYS* 3.1 40.6 + - + +
195A TRP* 3.0 26.3 + - + +
197A ASN* 1.3 76.6 - - + +
199A TYR* 1.3 57.6 + - - +
201A SER* 3.1 6.2 + - - -
202A SER* 2.6 39.1 + - - +
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Residues in contact with TYR 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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59A ILE* 4.8 0.7 - - - +
79A VAL* 3.8 24.1 - - + +
84A TYR* 3.4 47.4 + + + +
85A LEU* 5.8 2.0 - - + +
95A SER* 4.0 9.7 + - - -
195A TRP* 2.8 45.2 + + + +
196A ALA 3.6 2.7 - - - +
198A GLN* 1.3 77.6 - - - +
200A PHE* 1.3 73.9 + + - +
203A TYR* 2.8 60.0 + + + +
205A VAL* 3.6 36.9 - - + +
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Residues in contact with PHE 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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57A VAL* 4.0 11.9 - - + -
59A ILE* 4.3 5.8 - - + -
116A ALA* 3.9 21.3 - - + -
117A GLY* 3.3 28.7 - - - -
196A ALA 3.0 27.5 + - - +
199A TYR* 1.3 94.4 - + - +
201A SER* 1.3 58.2 + - - +
203A TYR 2.9 12.1 - - - +
204A SER 5.4 0.2 - - - -
205A VAL* 3.5 38.6 - - + -
299A PHE* 4.5 8.3 - + - -
300A ILE* 3.6 16.2 - - + -
302A SER* 3.5 17.3 - - - +
303A SER* 3.6 18.3 + - - -
304A LYS* 2.8 21.8 + - - +
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Residues in contact with SER 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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197A ASN 2.8 22.7 + - - -
198A GLN* 3.1 12.5 + - - -
200A PHE* 1.3 78.7 - - - +
202A SER* 1.3 61.0 + - - +
302A SER* 3.1 19.5 + - - -
304A LYS* 3.5 20.5 - - - +
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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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198A GLN* 2.6 25.7 + - - +
201A SER* 1.3 83.3 + - - +
203A TYR* 1.3 81.5 + - - +
304A LYS* 4.0 16.0 + - - -
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Residues in contact with TYR 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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84A TYR* 4.4 15.6 + + - -
85A LEU* 3.8 28.4 - - + +
88A GLN* 4.8 5.6 + - - -
93A ASP* 3.8 32.3 - - - +
199A TYR* 2.8 47.5 + + + +
200A PHE 2.9 21.1 - - - +
202A SER* 1.3 96.3 - - - +
204A SER* 1.3 64.9 + - - +
205A VAL* 3.3 8.2 + - - +
304A LYS* 4.0 9.1 + - - +
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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