Contacts of the helix formed by residues 164 - 182 (chain A) in PDB entry 5WXN
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 HIS 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU* 3.9 33.9 + - + +
160A MET* 3.3 29.9 - - + +
161A GLN* 3.2 19.1 + - + +
162A PRO 3.6 0.2 - - - -
163A THR* 1.3 78.7 + - - +
165A PRO* 1.3 91.8 - - + +
166A ILE* 3.5 20.4 - - + +
167A ARG 2.8 18.7 + - - +
168A LEU* 2.9 10.9 + - - +
210A SER* 5.2 1.6 - - - -
341C LEU* 4.4 8.3 - - - +
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Residues in contact with PRO 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR 3.1 9.4 - - - +
164A HIS* 1.3 96.6 - - + +
166A ILE* 1.3 55.1 + - - +
168A LEU* 4.4 4.3 - - + -
169A GLY* 2.8 25.1 + - - -
210A SER* 3.6 27.6 - - - +
213A ASP* 4.5 9.2 - - + -
214A SER* 4.0 9.9 - - - +
217A ILE* 3.3 25.4 - - + +
339C PRO* 3.4 4.5 - - + +
341C LEU* 3.6 33.0 - - + -
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Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 4.6 8.3 - - - +
113A GLU* 4.4 9.6 - - + +
116A VAL* 3.6 26.5 - - + +
117A PHE* 3.2 46.4 - - + +
120A LYS* 4.8 6.2 - - + +
160A MET* 3.9 12.1 - - + -
164A HIS* 3.0 25.1 - - + +
165A PRO* 1.3 80.0 - - - +
167A ARG* 1.3 60.5 + - - +
169A GLY 4.0 0.5 - - - -
170A LEU* 3.3 21.1 + - - +
339C PRO* 4.3 15.7 - - + +
341C LEU* 4.5 11.0 - - + -
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Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A SER* 3.4 45.6 + - - +
157A LYS* 3.5 30.5 + - - +
160A MET* 3.0 29.6 + - - -
161A GLN 3.7 18.2 - - - +
162A PRO* 3.8 30.6 + - + +
164A HIS* 2.8 9.1 + - + +
166A ILE* 1.3 78.9 - - - +
168A LEU* 1.3 59.6 + - - +
170A LEU* 3.4 6.4 + - - +
171A ALA* 3.2 23.0 + - - +
195A ALA* 5.9 1.4 - - - +
198A GLU* 3.3 29.7 + - - -
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO 3.4 19.5 - - - +
163A THR* 3.2 32.8 - - - +
164A HIS 2.9 11.3 + - - +
165A PRO* 4.4 1.8 - - + +
167A ARG* 1.3 72.8 - - - +
169A GLY* 1.3 61.9 + - - +
170A LEU 3.1 1.8 - - - -
171A ALA* 3.2 6.3 + - - +
172A LEU* 2.9 30.1 + - - +
195A ALA* 4.1 6.3 - - + +
199A ALA* 3.6 19.1 - - + -
214A SER* 3.8 26.2 - - - +
217A ILE* 3.6 14.9 - - + +
218A MET* 3.6 16.6 - - + -
221A LEU* 3.7 21.1 - - + +
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Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS* 3.9 9.6 - - - +
165A PRO 2.8 24.0 + - - -
166A ILE 4.0 1.3 - - - -
168A LEU* 1.3 73.1 - - - +
170A LEU* 1.3 60.2 + - - +
172A LEU* 3.9 1.2 - - - +
173A ASN* 3.2 29.8 + - - +
217A ILE* 3.9 3.5 - - - +
337C VAL* 3.8 23.8 - - - -
339C PRO* 4.5 4.7 - - - -
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 4.4 7.6 - - + -
120A LYS* 3.8 24.0 - - + -
149A TYR* 4.0 30.1 - - + +
152A ALA* 3.7 13.7 - - + +
153A PHE* 3.6 37.7 - - + +
156A SER* 4.1 8.5 - - - +
166A ILE 3.3 12.9 + - - +
167A ARG 3.5 8.5 - - - +
168A LEU 3.1 0.4 - - - -
169A GLY* 1.3 73.9 - - - +
171A ALA* 1.3 69.2 + - - +
173A ASN* 4.6 0.4 - - - +
174A PHE* 2.9 28.1 + - + +
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PHE* 5.4 7.0 - - + -
167A ARG 3.2 11.7 + - - +
168A LEU 3.2 8.3 + - - +
170A LEU* 1.3 83.0 - - - +
172A LEU* 1.3 58.2 + - - +
174A PHE* 4.4 0.4 - - - -
175A SER* 2.8 33.3 + - - -
191A LEU* 3.6 18.9 - - + +
195A ALA* 3.3 34.1 - - + -
221A LEU* 4.2 4.0 - - + -
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Residues in contact with LEU 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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168A LEU 2.9 16.3 + - - +
169A GLY 3.9 3.1 - - - +
171A ALA* 1.3 75.6 - - - +
173A ASN* 1.3 61.8 + - - +
175A SER* 2.6 20.0 + - - +
176A VAL* 3.0 13.6 + - - +
217A ILE* 4.4 6.3 - - + +
220A LEU* 3.4 46.2 - - + +
221A LEU* 3.5 20.1 - - + +
224A ASN* 3.3 24.7 - - + +
335C MET 3.7 16.4 - - - +
336C TPO 3.8 15.3 - - - -
337C VAL* 3.9 19.7 - - + +
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Residues in contact with ASN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS* 3.9 3.6 - - + +
124A ASP* 2.6 41.1 + - - +
127A ARG* 4.2 2.8 + - - +
149A TYR* 4.1 11.8 + - + +
169A GLY 3.2 14.1 + - - +
170A LEU 4.2 1.6 - - - +
172A LEU* 1.3 78.3 - - - +
174A PHE* 1.3 58.6 + - - +
176A VAL* 3.2 3.8 + - - +
177A PHE* 2.9 26.9 + - - +
336C TPO 3.3 31.7 + - + +
337C VAL 3.1 37.3 + - - +
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLN* 4.4 7.2 - - + -
149A TYR* 3.3 45.7 - + + -
150A GLN* 3.5 31.0 - - + -
153A PHE* 3.8 40.6 - + + -
170A LEU* 2.9 24.2 + - + +
171A ALA 3.8 2.5 - - - +
173A ASN* 1.3 74.0 - - - +
175A SER* 1.4 66.0 + - - +
177A PHE* 3.0 16.3 + + - +
178A TYR* 3.0 53.0 + + - -
191A LEU* 3.9 14.1 - - + -
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA 2.8 19.4 + - - -
172A LEU* 2.6 26.7 + - - +
174A PHE* 1.4 71.4 - - - +
176A VAL* 1.3 61.5 + - - +
178A TYR* 3.2 4.8 + - - -
179A TYR 3.0 17.8 + - - -
188A ALA* 3.2 39.3 - - - +
191A LEU* 4.3 5.0 - - - +
192A ALA* 4.0 16.4 - - - +
221A LEU* 4.7 0.3 - - - +
224A ASN* 5.4 0.3 - - - +
228A TRP* 3.4 16.6 - - - -
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 4.2 12.8 - - - +
172A LEU 3.0 15.8 + - - +
173A ASN 3.2 7.6 + - - +
175A SER* 1.3 75.7 - - - +
177A PHE* 1.3 54.2 + - - +
180A GLU* 2.6 55.6 + - + +
224A ASN* 3.5 14.4 - - - +
228A TRP* 3.6 15.3 - - + -
334C SER* 3.7 13.9 - - - +
335C MET 3.3 26.0 - - - +
336C TPO 4.0 16.6 - - + +
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Residues in contact with PHE 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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127A ARG* 4.2 11.2 - - + +
130A ALA* 5.7 0.2 - - + -
142A VAL* 3.7 23.3 - - + -
145A SER* 3.3 27.6 - - - -
146A GLN* 3.6 41.5 - - + -
149A TYR* 3.8 15.7 - + + -
173A ASN 2.9 13.3 + - - +
174A PHE* 3.2 24.7 - + - +
176A VAL* 1.3 77.4 - - - +
178A TYR* 1.3 68.4 + + - +
181A ILE* 2.9 54.2 + - + +
182A LEU* 3.2 22.8 + - + -
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Residues in contact with TYR 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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146A GLN* 3.2 30.6 + - - -
150A GLN* 4.1 6.6 + - - -
174A PHE* 3.0 55.1 + + - -
175A SER* 3.2 7.2 + - - +
177A PHE* 1.3 78.4 - + - +
179A TYR* 1.3 57.9 + - - +
182A LEU* 3.3 23.3 + - + -
183A ASN 3.0 24.9 + - - -
184A SER* 3.1 17.4 + - - +
187A LYS* 4.0 34.7 - - + +
188A ALA* 3.6 16.8 - - + +
191A LEU* 3.7 24.7 - - + -
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Residues in contact with TYR 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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175A SER 3.0 10.3 + - - +
176A VAL 3.9 0.7 - - - +
178A TYR* 1.3 80.1 - - - +
180A GLU* 1.3 75.5 + - + +
181A ILE 3.6 0.2 + - - -
183A ASN* 3.7 17.3 + - - +
184A SER 4.4 4.0 - - - +
185A PRO* 4.0 34.3 - - + +
188A ALA* 3.6 11.9 - - + +
227A LEU 5.3 0.5 + - - -
228A TRP* 3.4 73.7 + + + -
230A SER 5.5 2.1 + - - -
334C SER* 4.4 2.0 - - - -
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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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127A ARG* 5.5 1.0 + - - -
131A GLU* 4.1 16.0 - - - +
176A VAL* 2.6 31.6 + - + +
179A TYR* 1.3 83.0 - - + +
181A ILE* 1.3 70.3 + - + +
183A ASN* 4.8 0.7 - - - -
333C ARG* 4.4 13.7 + - - +
334C SER* 2.8 44.1 + - - +
336C TPO 5.7 0.5 + - - -
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 4.0 14.8 - - + +
130A ALA* 4.0 20.4 - - + +
131A GLU* 4.1 27.8 - - + +
138A LYS* 4.8 14.3 + - - +
142A VAL* 3.7 30.9 - - + +
177A PHE* 2.9 43.9 + - + +
180A GLU* 1.3 89.3 - - + +
182A LEU* 1.3 65.2 + - - +
183A ASN* 3.4 1.5 - - - +
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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
----------------------------------------------------------
142A VAL* 3.7 27.1 - - + -
146A GLN* 4.2 17.0 - - - +
177A PHE* 3.2 20.9 + - + +
178A TYR* 3.5 34.8 - - + +
181A ILE* 1.3 84.5 - - - +
183A ASN* 1.3 71.1 + - - +
184A SER* 3.0 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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