Contacts of the helix formed by residues 166 - 183 (chain A) in PDB entry 3P1S
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLU* 3.8 21.4 + - + +
162A MET* 4.1 20.2 - - + -
163A PRO* 3.0 39.3 + - + +
164A PRO 3.4 0.4 - - - -
165A THR* 1.3 79.0 + - - +
167A PRO* 1.3 79.3 - - + +
168A ILE* 3.0 52.7 + - + +
169A ARG* 3.0 7.0 + - + -
170A LEU* 2.9 19.9 + - - +
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Residues in contact with PRO 167 (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 THR 3.1 8.7 - - - +
166A HIS* 1.3 95.2 - - + +
168A ILE* 1.3 55.4 + - - +
170A LEU* 3.7 8.7 - - + +
171A GLY 2.8 24.1 + - - -
215A ASP* 4.0 36.8 - - + +
216A SER* 4.7 1.6 - - - +
219A ILE* 4.6 8.7 - - + +
249A FSC 3.5 36.6 - - + +
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 6.0 6.3 - - + -
41A ARG* 5.8 1.3 - - - +
115A GLU* 3.5 27.4 - - + +
118A VAL* 3.6 26.2 - - + -
119A PHE* 3.9 27.6 - - + +
122A LYS* 4.7 3.4 - - + +
162A MET* 3.9 8.1 - - + -
166A HIS* 3.0 28.6 + - + +
167A PRO* 1.3 77.8 - - + +
169A ARG* 1.3 64.7 + - - +
172A LEU* 2.9 25.0 + - + +
249A FSC 3.8 32.5 - - + +
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Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A MET* 5.3 3.8 - - + +
158A SER* 3.7 31.0 + - - +
159A LYS* 3.9 35.6 + - - +
162A MET* 2.9 41.3 + - - -
163A PRO 3.5 12.8 - - - +
164A PRO* 3.4 33.0 + - - +
166A HIS* 3.0 12.5 + - + +
168A ILE* 1.3 81.4 - - - +
170A LEU* 1.3 63.0 + - + +
172A LEU* 3.5 6.2 + - - +
173A ALA* 3.0 24.6 + - + +
197A THR* 5.8 4.1 - - + +
200A GLU* 3.8 20.8 + - - +
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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
----------------------------------------------------------
164A PRO 3.5 20.4 - - - +
165A THR* 3.5 22.9 - - - +
166A HIS 2.9 16.1 + - - +
167A PRO* 3.7 3.6 - - + +
169A ARG* 1.3 76.3 - - - +
171A GLY* 1.3 58.8 - - - +
173A ALA* 3.3 2.8 + - - +
174A LEU* 2.9 28.6 + - - +
197A THR* 3.6 24.5 - - + -
201A ALA* 3.7 13.2 - - + -
216A SER* 3.5 31.4 - - - +
219A ILE* 3.6 20.2 - - + +
220A MET* 4.0 7.9 - - + -
223A LEU* 4.1 14.0 - - + +
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Residues in contact with GLY 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LYS* 3.4 14.8 - - - -
167A PRO 2.8 19.9 + - - -
168A ILE 3.9 0.7 - - - -
170A LEU* 1.3 70.6 - - - +
172A LEU* 1.3 67.4 + - - +
174A LEU* 3.4 3.7 + - - +
175A ASN* 3.0 20.6 + - - +
219A ILE* 3.7 4.7 - - - +
249A FSC 4.1 4.9 - - - -
374P VAL* 3.4 24.9 - - - -
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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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118A VAL* 3.8 9.9 - - + -
122A LYS* 3.7 24.0 - - + +
151A TYR* 3.6 34.1 - - + +
154A ALA* 3.4 49.6 - - + +
155A MET* 3.5 19.5 - - - +
158A SER* 3.7 10.3 - - - +
168A ILE 2.9 17.5 + - - +
169A ARG 3.6 2.9 - - - +
171A GLY* 1.3 76.8 - - - +
173A ALA* 1.3 59.0 + - - +
175A ASN* 3.2 1.4 + - - +
176A PHE* 2.8 32.4 + - + +
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Residues in contact with ALA 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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155A MET* 4.3 14.8 - - + -
169A ARG* 3.0 19.6 + - + +
170A LEU 3.7 0.7 - - - +
172A LEU* 1.3 77.3 - - - +
174A LEU* 1.3 63.9 + - - +
176A PHE 4.5 0.2 - - - +
177A SER* 2.9 27.9 + - - -
193A LEU* 3.7 12.6 - - + +
197A THR* 3.3 38.6 - - + +
223A LEU* 4.5 1.8 - - - -
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Residues in contact with LEU 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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170A LEU 2.9 14.4 + - - +
171A GLY* 3.5 8.3 - - - +
173A ALA* 1.3 77.2 - - - +
175A ASN* 1.3 57.1 + - - +
177A SER* 3.3 4.4 + - - -
178A VAL* 3.0 27.2 + - - +
194A ALA* 6.3 0.2 - - + -
219A ILE* 4.8 2.9 - - + -
222A LEU* 3.6 46.4 - - + +
223A LEU* 3.6 30.8 - - + +
226A ASN* 3.5 25.5 + - - +
372P LYS 3.7 6.7 - - - +
373P SEP 3.7 26.7 - - - -
374P VAL* 3.8 9.6 - - + -
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Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 4.5 0.2 - - - +
122A LYS* 3.3 7.7 - - - +
126A ASP* 2.9 30.5 + - - +
129A ARG* 3.3 18.7 + - - +
151A TYR* 3.8 9.2 - - + +
171A GLY 3.0 16.4 + - - +
172A LEU 3.9 2.2 - - - +
174A LEU* 1.3 74.3 - - - +
176A PHE* 1.4 61.1 + - - +
178A VAL* 3.2 8.3 + - - +
179A PHE* 2.9 26.9 + - - +
373P SEP 3.3 10.1 + - - +
374P VAL 2.7 46.5 + - - +
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 4.3 14.8 - - + -
151A TYR* 3.5 39.4 - + + -
152A GLN* 3.7 25.6 - - - -
155A MET* 3.4 30.3 - - + -
172A LEU* 2.8 19.2 + - + +
173A ALA* 4.5 0.4 - - - -
175A ASN* 1.4 76.3 - - - +
177A SER* 1.3 57.9 + - - +
179A PHE* 3.2 23.9 - + - +
180A HIS* 2.9 56.2 + + - -
193A LEU* 3.9 18.6 - - + -
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ALA 2.9 19.9 + - - -
174A LEU* 3.5 6.5 + - - -
176A PHE* 1.3 77.2 - - - +
178A VAL* 1.3 56.3 + - - +
180A HIS* 3.1 2.1 + - - -
181A TYR* 2.9 24.3 + - - +
190A ALA* 2.8 41.9 + - - +
193A LEU* 3.7 14.9 - - - +
194A ALA* 3.7 10.9 - - - +
226A ASN* 5.4 0.6 + - - -
230A TRP* 3.2 18.0 - - - -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 3.8 13.5 - - - +
174A LEU 3.0 17.0 + - - +
175A ASN* 3.2 9.8 + - - +
177A SER* 1.3 76.8 - - - +
179A PHE* 1.3 62.4 + - - +
181A TYR* 3.1 1.3 + - - +
182A GLU* 2.9 31.6 + - + +
226A ASN* 3.6 12.3 - - - +
230A TRP* 4.0 8.5 - - + -
371P ARG* 3.6 45.1 - - + +
372P LYS 3.2 28.5 - - - +
373P SEP 4.6 2.5 - - - +
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Residues in contact with PHE 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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129A ARG* 3.9 14.8 - - + +
144A ILE* 3.5 32.1 - - + -
147A ALA* 3.6 28.0 - - + -
148A ARG* 3.8 22.4 - - + -
151A TYR* 3.8 16.6 - + + -
175A ASN 2.9 13.3 + - - +
176A PHE* 3.2 30.3 - + - +
178A VAL* 1.3 76.0 - - - +
180A HIS* 1.3 71.5 + + - +
183A ILE* 2.9 39.3 + - + +
184A ALA* 2.9 38.9 + - + -
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Residues in contact with HIS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 5.7 2.5 - - + -
176A PHE* 2.9 58.3 + + - -
177A SER* 3.1 7.2 + - - +
179A PHE* 1.3 88.3 - + - +
181A TYR* 1.3 62.8 + - - +
184A ALA* 4.1 6.1 - - - +
185A ASN 3.4 4.3 + - - -
186A SER* 2.8 45.9 + - - +
189A GLU* 3.5 37.5 + - + +
190A ALA 3.6 5.6 - - - +
193A LEU* 4.0 17.3 - - + +
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Residues in contact with TYR 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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177A SER 2.9 16.5 + - - +
178A VAL* 3.6 4.3 - - - +
180A HIS* 1.3 79.9 - - - +
182A GLU* 1.3 69.3 - - + +
185A ASN* 4.3 9.5 + - - -
186A SER 4.4 0.9 + - - -
187A PRO* 3.7 39.1 - - + +
190A ALA* 3.6 7.4 - - + -
191A ILE* 4.8 2.5 - - + -
230A TRP* 3.4 75.4 + + + +
371P ARG* 6.1 0.4 - - + -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 4.8 0.5 + - - -
133A GLU* 3.8 11.8 - - + +
178A VAL* 2.9 17.6 + - + +
181A TYR* 1.3 88.1 - - + +
183A ILE* 1.3 77.4 + - + +
185A ASN 4.8 1.3 - - - -
370P ARG* 4.7 7.3 + - - -
371P ARG* 2.8 50.9 + - - +
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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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129A ARG* 3.9 30.1 - - + +
132A ALA* 3.7 12.6 - - + +
133A GLU* 3.9 35.0 - - + +
140A LYS* 5.2 3.5 + - - +
144A ILE* 3.6 39.0 - - + +
179A PHE* 2.9 30.8 + - + +
182A GLU* 1.3 98.2 - - + +
184A ALA* 1.3 61.7 + - - +
185A ASN* 3.4 3.4 + - - +
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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