Contacts of the helix formed by residues 157 - 173 (chain B) in PDB entry 4MSP
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 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ASP* 3.3 33.1 + - + +
155B VAL* 3.7 5.8 + - + +
156B VAL* 1.3 71.1 - - - +
158B GLU* 1.3 64.5 + - - +
159B SER* 2.7 28.2 + - - -
160B HIS* 2.9 24.0 + - - +
161B HIS* 3.0 25.9 + - - -
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LYS* 2.7 33.7 + - - +
156B VAL* 3.5 15.6 + - + +
157B ASN* 1.3 72.4 + - - +
159B SER* 1.3 58.2 + - - +
161B HIS* 3.2 3.6 + - - +
162B ASP* 2.8 42.1 + - - +
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ASN* 2.7 21.8 + - - -
158B GLU* 1.3 78.2 - - - +
160B HIS* 1.3 67.4 + - - +
162B ASP* 3.5 7.7 + - - +
163B ALA* 3.0 25.6 + - - +
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Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A HIS* 4.7 2.9 + - - -
163A ALA* 3.8 31.8 + - + +
164A LEU* 4.3 13.6 - - + +
166A GLU* 6.2 0.4 - - + -
167A ASP* 2.7 41.6 + - - +
157B ASN* 2.9 29.7 + - - +
159B SER* 1.3 81.7 + - - +
161B HIS* 1.3 59.0 + - - +
163B ALA* 3.5 5.5 + - + +
164B LEU* 3.0 28.1 + - - +
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Residues in contact with HIS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 3.7 25.4 - - + +
142B LYS* 5.2 12.0 + - + -
145B LEU* 3.7 32.6 - - + +
146B LYS* 4.4 1.6 + - - +
149B PHE* 3.7 42.1 - + - -
155B VAL 4.8 0.4 + - - -
156B VAL* 3.7 30.0 - - + +
157B ASN 3.0 25.7 + - - +
158B GLU* 3.7 7.6 - - - +
160B HIS* 1.3 75.5 - - + +
162B ASP* 1.3 62.1 + - - +
164B LEU* 3.2 8.2 + - + +
165B VAL* 2.8 36.8 + - - +
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Residues in contact with ASP 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 3.1 37.5 + - - +
158B GLU* 2.8 35.3 + - - +
159B SER* 3.9 6.8 - - - +
161B HIS* 1.3 72.7 - - - +
163B ALA* 1.3 57.7 + - - +
165B VAL* 3.4 6.9 + - - +
166B GLU* 2.9 36.2 + - + +
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A HIS* 3.9 11.0 - - + +
159B SER 3.0 18.7 + - - +
160B HIS* 3.7 5.6 - - - +
162B ASP* 1.3 74.2 - - - +
164B LEU* 1.3 65.2 + - - +
166B GLU* 3.4 7.3 + - - +
167B ASP* 3.1 28.5 + - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PHE* 3.5 29.4 - - + -
156A VAL* 3.6 39.9 - - + -
160A HIS* 3.6 24.2 - - + +
164A LEU* 4.2 13.0 - - + -
145B LEU* 3.8 22.9 - - + -
160B HIS 3.0 18.1 + - - +
161B HIS* 3.5 9.9 - - + +
163B ALA* 1.3 74.3 - - - +
165B VAL* 1.3 65.5 + - - +
167B ASP* 3.2 2.6 + - - +
168B ILE* 2.9 37.5 + - + +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LYS* 3.9 37.0 - - + +
141B VAL* 4.2 4.0 - - + -
142B LYS* 4.0 23.8 - - + +
145B LEU* 3.6 24.9 - - + -
161B HIS 2.8 24.7 + - - +
162B ASP* 3.8 7.4 - - - +
164B LEU* 1.3 72.5 - - - +
166B GLU* 1.3 65.5 + - - +
168B ILE* 3.2 7.1 + - - +
169B PHE* 3.0 36.9 + - + -
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS* 2.9 42.5 + - - +
162B ASP* 2.9 21.9 + - + +
163B ALA* 3.7 8.3 - - - +
164B LEU 3.3 0.2 - - - -
165B VAL* 1.3 77.0 - - - +
167B ASP* 1.3 60.4 + - - +
169B PHE* 3.5 2.7 + - - +
170B ASP* 3.0 44.0 + - - +
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A VAL* 5.6 4.5 - - + -
160A HIS* 2.6 38.6 + - + +
163B ALA* 3.1 11.4 + - - +
164B LEU 3.8 2.0 - - - +
165B VAL 3.2 0.2 - - - -
166B GLU* 1.3 75.1 - - - +
168B ILE* 1.3 66.5 + - + +
170B ASP* 3.4 16.2 + - - +
171B LYS* 3.2 23.4 + - - +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PHE* 5.7 0.2 - - + -
154A ALA* 4.1 20.4 - - + -
156A VAL* 3.7 21.5 - - + -
204A 1PE 4.6 9.0 - - - +
206A PGO 4.0 19.5 - - + -
141B VAL* 4.6 9.9 - - + -
145B LEU* 4.7 3.1 - - + -
164B LEU* 2.9 43.2 + - + +
165B VAL* 3.5 8.7 - - - +
167B ASP* 1.3 76.3 - - - +
169B PHE* 1.3 64.4 + - + +
171B LYS* 3.2 4.7 + - - -
172B GLU* 2.8 49.3 + - + +
180B ILE* 4.2 8.3 - - + -
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LEU 3.4 15.9 - - - -
137B SER 3.5 23.6 - - - -
138B LYS* 3.5 35.0 - - + -
141B VAL* 3.6 31.2 - - + -
165B VAL* 3.0 23.5 + - + +
166B GLU 4.0 2.9 - - - +
168B ILE* 1.3 78.7 - - + +
170B ASP* 1.3 66.6 + - - +
173B ASP* 2.8 40.0 + - + +
176B LYS* 3.8 1.4 + - - -
178B GLY 3.4 30.5 - - - -
180B ILE* 3.8 29.2 - - + -
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLU* 3.0 34.6 + - - +
167B ASP* 3.6 20.1 - - - +
169B PHE* 1.3 75.1 - - - +
171B LYS* 1.3 59.1 + - - +
176B LYS* 2.7 26.9 + - - +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 3.0 43.6 + - - +
156A VAL* 6.2 0.4 - - + -
167B ASP 3.2 13.7 + - - +
168B ILE* 3.7 4.0 - - - +
169B PHE 3.1 0.6 - - - -
170B ASP* 1.3 82.2 - - - +
172B GLU* 1.3 82.3 + - - +
173B ASP 3.6 1.3 - - - -
174B GLU* 5.2 2.4 + - - +
176B LYS* 5.2 0.4 + - - -
189B HIS 6.0 1.1 - - - -
190B ASP* 3.8 27.2 + - - +
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLY 4.2 8.7 - - - +
154A ALA* 5.2 0.3 - - - -
155A VAL* 4.7 6.9 + - - +
206A PGO 3.9 15.3 - - - -
168B ILE* 2.8 28.8 + - + +
171B LYS* 1.3 104.1 - - - +
173B ASP* 1.3 60.5 + - - +
174B GLU* 2.9 11.9 + - - +
180B ILE* 3.7 18.8 - - + -
184B GLU* 3.8 19.6 - - - +
188B LYS* 2.5 44.0 + - - +
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Residues in contact with ASP 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 2.8 32.6 + - + +
171B LYS 5.1 0.7 - - - -
172B GLU* 1.3 72.8 - - - +
174B GLU* 1.3 61.3 + - - +
175B ASP* 3.1 6.9 - - - +
176B LYS* 2.9 38.4 + - - +
177B ASP* 3.2 0.5 - - - +
178B GLY* 2.9 27.5 + - - -
179B PHE 3.3 19.3 - - - +
180B ILE* 4.3 1.5 - - + +
184B GLU* 4.2 1.6 - - - -
202B CA 2.3 28.9 - - - -
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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