Contacts of the helix formed by residues 157 - 173 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A VAL* 1.3 79.3 - - - +
158A GLU* 1.3 70.4 + - - +
159A SER* 2.4 40.0 + - - +
160A HIS* 2.9 31.9 + - + +
161A HIS* 3.7 2.5 + - - -
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Residues in contact with GLU 158 (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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142A LYS* 3.0 23.4 + - + +
146A LYS* 2.7 41.0 + - - -
156A VAL 3.8 2.2 + - - +
157A ASN* 1.3 79.3 - - - +
159A SER* 1.3 57.1 + - - +
161A HIS* 3.0 8.8 + - - -
162A ASP* 2.8 43.2 + - - +
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASN* 2.4 28.9 + - - +
158A GLU* 1.3 77.7 - - - +
160A HIS* 1.3 64.9 + - - +
162A ASP* 3.5 8.6 + - - +
163A ALA* 2.9 30.5 + - - +
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Residues in contact with HIS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A VAL* 3.9 19.7 - - + -
157A ASN* 2.9 39.2 + - + +
159A SER* 1.3 84.9 + - - +
161A HIS* 1.3 63.0 + - - +
163A ALA* 3.1 6.1 + - - +
164A LEU* 2.9 33.4 + - + +
160B HIS 4.7 3.4 + - - -
163B ALA* 3.7 11.6 - - + +
164B LEU* 3.6 38.6 + - + +
167B ASP* 2.6 36.3 + - + +
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Residues in contact with HIS 161 (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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142A LYS* 3.9 20.9 - - + -
145A LEU* 3.9 19.3 - - + +
146A LYS* 3.7 41.8 - - + +
149A PHE* 3.4 42.3 - + + +
156A VAL* 3.5 25.1 + - + +
157A ASN 4.0 12.8 - - - -
158A GLU* 3.0 9.4 + - - +
160A HIS* 1.3 74.8 - - - +
162A ASP* 1.3 57.3 + - - +
164A LEU* 3.3 5.5 + - - +
165A VAL* 2.9 37.1 + - - +
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Residues in contact with ASP 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 2.8 32.4 + - - +
158A GLU* 2.8 29.9 + - - +
159A SER* 3.8 7.8 - - - +
161A HIS* 1.3 76.0 - - - +
163A ALA* 1.3 61.8 + - - +
165A VAL* 3.6 6.2 + - - +
166A GLU* 3.2 28.2 + - - +
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER 2.9 18.8 + - - +
160A HIS* 3.1 6.7 + - - +
162A ASP* 1.3 77.8 - - - +
164A LEU* 1.3 61.4 + - - +
166A GLU* 3.3 7.2 + - - +
167A ASP* 3.1 28.2 + - - +
160B HIS* 3.8 31.3 + - + +
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Residues in contact with LEU 164 (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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145A LEU* 4.0 12.3 - - + -
149A PHE* 3.6 35.4 - - + -
160A HIS* 2.9 25.8 + - + +
161A HIS* 3.8 6.3 - - - +
163A ALA* 1.3 72.9 - - - +
165A VAL* 1.3 65.7 + - - +
167A ASP* 3.2 16.7 + - - +
168A ILE* 3.0 28.7 + - - +
149B PHE* 3.9 15.4 - - + -
160B HIS* 4.3 12.6 - - + +
161B HIS* 3.7 35.0 - - + +
164B LEU* 4.2 10.8 - - + -
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Residues in contact with VAL 165 (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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138A LYS* 3.7 37.5 - - + +
141A VAL* 4.2 4.5 - - + -
142A LYS* 3.8 35.9 - - + +
145A LEU* 3.9 10.3 - - + -
161A HIS 2.9 20.6 + - - +
162A ASP* 3.8 7.4 - - - +
164A LEU* 1.3 77.6 - - - +
166A GLU* 1.3 58.0 + - - +
168A ILE* 3.2 7.4 + - - +
169A PHE* 2.9 43.7 + - + -
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Residues in contact with GLU 166 (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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138A LYS* 2.7 40.8 + - - +
162A ASP* 3.2 15.9 + - + +
163A ALA* 3.7 9.2 - - - +
164A LEU 3.3 0.2 - - - -
165A VAL* 1.3 74.5 - - + +
167A ASP* 1.3 68.1 + - - +
169A PHE* 4.2 4.1 - - - +
170A ASP* 2.9 26.3 + - - +
160B HIS* 6.2 0.2 - - + -
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Residues in contact with ASP 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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163A ALA 3.1 11.0 + - - +
164A LEU* 3.2 18.9 + - + +
166A GLU* 1.3 76.9 - - - +
168A ILE* 1.3 63.5 + - + +
170A ASP* 3.4 15.1 - - - +
171A LYS 3.9 1.0 + - - -
149B PHE* 6.0 0.2 - - + -
155B VAL* 3.1 38.7 - - + +
157B ASN* 3.3 23.6 + - + +
160B HIS* 2.7 40.2 + - - +
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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
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141A VAL* 4.1 20.6 - - + -
145A LEU* 4.3 8.5 - - + -
164A LEU 3.0 19.1 + - - +
165A VAL* 3.5 6.3 - - - +
167A ASP* 1.3 78.8 - - + +
169A PHE* 1.3 62.8 + - + +
171A LYS* 3.3 5.5 + - - +
172A GLU* 3.1 35.7 + - + +
180A ILE* 4.3 10.3 - - + -
204A 1PE 4.1 31.9 - - - +
149B PHE* 4.3 16.2 - - + -
154B ALA* 3.8 27.8 - - + +
155B VAL* 4.6 6.7 - - - +
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Residues in contact with PHE 169 (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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136A LEU 3.5 19.1 - - - -
137A SER 3.7 2.2 - - - -
138A LYS* 3.6 32.5 - - + -
141A VAL* 3.7 20.2 - - + -
165A VAL* 2.9 43.3 + - + +
166A GLU* 4.2 5.4 - - - +
168A ILE* 1.3 73.4 - - + +
170A ASP* 1.3 66.7 + - - +
171A LYS 3.1 2.2 - - - -
172A GLU* 3.8 1.1 - - - -
173A ASP* 3.0 49.6 + - + +
176A LYS* 3.6 2.3 + - - -
178A GLY 3.2 29.8 - - - -
180A ILE* 3.6 30.3 - - + -
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Residues in contact with ASP 170 (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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166A GLU 2.9 18.7 + - - +
167A ASP* 3.4 11.8 - - - +
168A ILE 3.2 0.2 - - - -
169A PHE* 1.3 75.4 - - - +
171A LYS* 1.3 66.0 + - + +
176A LYS* 3.1 25.9 + - - +
155B VAL* 5.8 1.0 - - - +
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Residues in contact with LYS 171 (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 ASP 3.9 1.7 + - - +
168A ILE 3.3 7.4 + - - +
169A PHE 3.1 0.4 - - - -
170A ASP* 1.3 89.5 - - - +
172A GLU* 1.3 70.9 + - + +
173A ASP 3.6 1.2 - - - +
174A GLU* 4.3 12.3 - - - +
189A HIS* 4.8 13.6 + - - +
190A ASP* 3.4 46.2 + - - +
153B GLY 4.3 11.6 + - - +
155B VAL* 3.6 40.6 - - + +
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Residues in contact with GLU 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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120A ARG* 2.7 38.9 + - - +
168A ILE* 3.1 27.7 + - + +
171A LYS* 1.3 85.4 + - + +
173A ASP* 1.3 61.6 + - - +
174A GLU* 3.5 4.3 + - - +
180A ILE* 3.6 26.4 - - + +
184A GLU* 3.3 33.6 - - - +
185A PHE* 4.7 0.5 - - - -
188A LYS* 4.4 5.9 - - - -
189A HIS* 4.5 3.7 + - - -
203A CA 2.6 29.2 - - - -
204A 1PE 4.8 1.8 - - - +
153B GLY 3.4 12.8 - - - +
154B ALA* 6.1 0.4 - - - -
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Residues in contact with ASP 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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138A LYS* 5.7 0.3 - - - -
169A PHE* 3.0 30.2 + - + +
170A ASP 4.3 1.0 - - - +
171A LYS 4.6 1.0 - - - +
172A GLU* 1.3 76.5 - - - +
174A GLU* 1.3 55.2 + - - +
176A LYS* 2.6 59.5 + - + +
177A ASP* 3.4 0.5 - - - +
178A GLY* 2.9 30.0 + - - -
179A PHE 3.1 16.4 - - - +
180A ILE* 4.3 1.0 - - - +
184A GLU* 3.7 1.6 - - - -
202A CA 2.3 28.4 - - - -
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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
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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