Contacts of the helix formed by residues 171 - 186 (chain A) in PDB entry 4WPN
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 PHE 171 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 4.4 0.4 - - - -
113A LYS* 3.3 14.4 - - - +
122A ASP* 3.3 25.1 - - - -
168A PRO 4.4 1.5 + - - -
170A ASN* 1.3 96.4 + - - +
172A PRO* 1.3 62.0 - - - +
173A LEU 3.4 2.0 - - - -
174A VAL* 4.1 12.6 - - + -
175A MET* 2.9 42.3 + - + +
297A TYR* 4.1 10.3 - + - -
298A HIS* 3.8 12.8 - + + -
301A GLN 3.8 19.5 - - - -
302A CYS* 3.7 20.4 - - - -
303A CYS* 6.5 0.2 - - - -
601A 3ST 3.4 54.1 - - + -
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Residues in contact with PRO 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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107A GLU* 3.4 28.5 - - + +
111A GLY* 5.5 3.6 - - - -
113A LYS* 4.6 4.7 - - - -
167A ILE* 3.5 7.9 - - + +
168A PRO 3.8 10.3 - - - +
169A TRP 3.3 19.5 - - - +
170A ASN 3.5 3.6 - - - +
171A PHE* 1.3 87.6 - - - +
173A LEU* 1.3 57.4 + - - +
176A LEU* 3.1 29.2 + - - +
198A THR* 3.6 35.0 - - + +
201A THR* 3.8 9.0 - - - +
202A ALA* 6.0 1.3 - - - +
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Residues in contact with LEU 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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96A ILE* 5.6 2.7 - - + -
103A LEU* 4.0 21.3 - - + +
107A GLU* 3.0 25.0 + - - +
122A ASP* 5.8 0.7 - - + -
123A LEU* 3.6 35.4 - - + -
126A CYS* 3.2 22.3 - - + -
172A PRO* 1.3 74.0 - - - +
174A VAL* 1.3 67.8 + - + +
176A LEU* 3.3 8.5 + - + +
177A ILE* 3.0 26.0 + - + +
201A THR* 4.0 19.9 + - + +
205A VAL* 3.3 33.9 - - + -
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Residues in contact with VAL 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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107A GLU* 4.5 0.4 + - - -
122A ASP* 3.4 50.5 - - + +
126A CYS* 3.4 11.2 - - - +
171A PHE* 3.6 11.1 + - + -
172A PRO 3.5 0.4 - - - -
173A LEU* 1.3 77.0 - - - +
175A MET* 1.3 70.0 + - + +
177A ILE* 3.2 4.3 + - - +
178A TRP* 2.8 55.1 + - + +
601A 3ST 3.8 31.2 - - + +
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Residues in contact with MET 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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167A ILE* 3.7 4.9 - - + -
168A PRO* 3.7 32.3 - - + -
170A ASN* 4.7 1.1 - - - +
171A PHE* 2.9 28.7 + - + +
174A VAL* 1.3 86.1 - - + +
176A LEU* 1.3 66.0 + - - +
178A TRP* 3.3 53.8 - - + +
179A LYS* 3.1 35.7 + - + +
245A THR* 4.5 23.8 - - - -
269A GLU* 6.4 0.4 - - - -
477A GLU* 5.4 0.9 - - - +
601A 3ST 4.3 14.4 - - + -
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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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167A ILE* 3.7 12.9 - - + +
172A PRO 3.1 20.9 + - - +
173A LEU* 3.5 7.9 - - + +
175A MET* 1.3 75.2 - - - +
177A ILE* 1.3 64.9 + - + +
179A LYS* 3.2 4.2 + - - +
180A ILE* 2.9 45.5 + - + +
192A VAL* 3.7 30.7 - - + -
202A ALA* 3.8 34.5 - - + +
205A VAL* 3.9 30.3 - - + -
219A VAL* 6.3 0.2 - - + -
221A ILE* 5.2 6.5 - - + -
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Residues in contact with ILE 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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92A LEU* 5.9 0.2 - - + -
96A ILE* 4.3 17.9 - - + -
126A CYS* 3.6 34.5 - - + +
129A THR* 3.8 14.5 - - + +
130A LEU* 3.8 39.9 - - + +
173A LEU* 3.0 22.9 + - + +
174A VAL 3.7 7.2 - - - +
176A LEU* 1.3 93.0 - - + +
178A TRP* 1.3 60.4 + - - +
180A ILE* 4.2 13.0 - - + -
181A GLY* 3.0 26.2 + - - -
182A PRO* 3.8 1.0 - - - +
205A VAL* 4.8 2.9 - - + -
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Residues in contact with TRP 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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126A CYS* 6.4 0.2 - - - -
129A THR* 3.9 20.0 + - + -
174A VAL* 2.8 33.6 + - + +
175A MET* 3.3 38.8 + - + +
177A ILE* 1.3 73.6 - - + +
179A LYS* 1.3 61.4 + - + +
182A PRO* 3.1 23.7 - - - +
269A GLU* 5.9 0.2 - - + -
460A VAL* 3.6 32.5 - - + -
461A SER 6.1 0.2 - - - -
466A PHE* 3.7 37.9 - + + -
477A GLU* 3.9 33.2 - - + +
478A LEU* 3.3 31.4 - - + +
486A TYR* 5.4 2.1 - - - -
601A 3ST 3.0 35.7 + - + -
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Residues in contact with LYS 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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165A GLN* 3.0 48.3 + - + +
166A ILE 4.6 5.2 - - - -
167A ILE* 4.0 14.8 - - + -
168A PRO* 5.7 0.4 - - - -
175A MET* 3.1 29.7 + - - +
176A LEU 3.5 3.1 - - - +
177A ILE 3.1 0.2 - - - -
178A TRP* 1.3 80.6 - - + +
180A ILE* 1.3 65.9 + - + +
181A GLY 3.4 0.5 + - - -
182A PRO* 3.6 0.3 - - - +
183A ALA 3.4 13.5 + - - -
243A ALA* 4.2 20.0 - - + -
244A PHE 4.5 7.2 + - - +
245A THR* 2.5 36.1 + - - +
477A GLU* 2.6 31.2 + - - +
486A TYR* 4.3 5.8 + - - +
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Residues in contact with ILE 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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92A LEU* 4.5 13.7 - - + -
130A LEU* 5.4 2.9 - - + -
165A GLN* 3.5 17.9 - - - +
176A LEU* 2.9 51.2 + - + +
177A ILE* 4.2 14.1 - - + -
179A LYS* 1.3 71.1 - - + +
181A GLY* 1.3 64.6 + - - +
183A ALA* 4.4 2.9 - - - -
184A LEU* 2.9 53.6 + - + +
190A VAL* 4.3 7.4 - - + -
192A VAL* 3.9 12.3 - - + -
205A VAL* 4.8 2.7 - - + -
209A ILE* 4.1 25.4 - - + -
219A VAL* 5.0 2.2 - - + -
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Residues in contact with GLY 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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89A LEU* 4.0 5.0 - - - +
130A LEU* 4.4 14.6 - - - -
133A CYS* 3.7 19.3 - - - +
177A ILE 3.0 16.5 + - - -
180A ILE* 1.3 80.4 - - - +
182A PRO* 1.3 61.4 - - - +
185A SER* 3.0 30.1 + - - -
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Residues in contact with PRO 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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133A CYS* 3.6 17.0 - - - -
177A ILE 3.8 0.7 - - - +
178A TRP* 3.1 30.3 - - - +
179A LYS 3.6 2.2 - - - +
181A GLY* 1.3 86.0 - - - +
183A ALA* 1.3 62.2 + - - +
185A SER* 3.3 0.7 + - - -
186A CYS* 3.1 29.3 + - - -
477A GLU* 6.3 0.2 - - + -
478A LEU* 4.2 17.3 - - + +
482A GLY 4.9 3.6 - - - +
483A PHE* 3.7 28.7 - - + -
486A TYR* 3.9 22.0 - - + -
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Residues in contact with ALA 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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165A GLN* 3.7 15.7 - - - +
179A LYS 3.4 17.4 + - - +
180A ILE 3.9 1.8 - - - +
181A GLY 3.3 1.0 - - - -
182A PRO* 1.3 79.4 - - - +
184A LEU* 1.3 61.4 + - - +
187A GLY 3.2 3.1 + - - -
188A ASN* 3.0 37.3 + - + +
190A VAL* 3.8 18.8 - - + -
486A TYR* 3.7 24.6 - - + -
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Residues in contact with LEU 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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77A TRP* 3.4 22.7 - - + -
85A ARG* 3.5 5.4 + - - +
89A LEU* 4.0 26.0 - - + -
92A LEU* 5.7 0.7 - - + -
180A ILE* 2.9 39.8 + - + +
183A ALA* 1.3 71.7 - - - +
185A SER* 1.3 67.3 + - - +
186A CYS 3.1 1.8 - - - -
187A GLY 3.0 9.7 + - - -
188A ASN 3.5 12.3 - - - +
190A VAL* 4.7 7.0 - - + -
209A ILE* 5.5 0.7 - - + -
214A PHE* 4.2 10.5 - - + -
218A VAL* 3.4 35.9 - - + +
219A VAL* 3.7 25.1 - - + -
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Residues in contact with SER 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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85A ARG* 2.8 32.0 + - - +
89A LEU* 3.7 12.7 - - - +
133A CYS 2.7 27.7 + - - -
136A TRP* 3.6 0.5 - - - +
137A ALA* 3.1 29.6 + - - +
140A ILE* 4.9 1.0 - - - +
181A GLY 3.0 20.1 + - - -
182A PRO 3.3 0.6 + - - -
184A LEU* 1.3 75.1 - - - +
186A CYS* 1.3 51.7 + - - +
483A PHE* 3.5 20.2 - - - -
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Residues in contact with CYS 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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85A ARG* 3.8 9.9 + - - +
140A ILE* 4.3 12.1 - - - +
157A HIS 5.2 1.4 - - - +
158A GLU 4.7 0.2 - - - -
159A PRO* 3.4 22.3 - - - +
182A PRO 3.1 20.6 + - - +
185A SER* 1.3 75.6 - - - +
187A GLY* 1.3 57.3 + - - +
188A ASN* 3.6 5.2 - - - +
483A PHE* 3.6 43.5 - - - -
486A TYR* 3.6 22.9 - - - +
487A THR* 3.9 14.8 - - + +
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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