Contacts of the helix formed by residues 163 - 176 (chain A) in PDB entry 4M3P
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLN* 4.4 5.6 + - - -
161A PHE* 4.3 1.8 - - - +
162A GLU* 1.3 83.0 - - + +
164A VAL* 1.3 66.6 + - - +
165A GLU* 3.1 4.8 + - + +
166A GLU* 3.1 33.8 + - + +
167A ALA* 3.1 11.6 + - - +
185A MET* 3.5 3.5 - - - +
192A ASP* 3.5 3.8 - - - -
193A LEU* 3.7 36.7 - - + +
194A HIS* 3.4 43.3 - + + +
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Residues in contact with VAL 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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163A HIS* 1.3 71.5 - - - +
165A GLU* 1.3 60.7 + - + +
167A ALA* 4.1 1.1 - - - -
168A VAL* 2.8 36.7 + - + +
185A MET* 3.3 18.6 - - - +
192A ASP* 2.9 18.8 + - - +
194A HIS* 6.3 0.7 - - + -
196A VAL* 4.1 11.7 - - + -
201A CYS* 3.6 48.7 - - + +
204A ARG* 3.6 32.5 - - + +
205A LEU* 4.3 8.3 - - + -
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Residues in contact with GLU 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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163A HIS* 3.1 6.6 - - + +
164A VAL* 1.3 83.9 - - + +
166A GLU* 1.3 61.4 + - - +
168A VAL* 3.3 5.5 + - - +
169A TRP* 3.1 60.9 + - + +
192A ASP* 4.7 0.2 + - - -
194A HIS* 4.5 18.6 + - + -
204A ARG* 4.3 15.7 - - - +
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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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124A GLN* 3.4 21.6 - - - +
125A THR* 2.8 50.5 + - - +
137A VAL* 4.0 19.2 - - + +
141A PHE* 3.8 1.7 - - + -
161A PHE* 3.8 8.6 - - + -
163A HIS* 3.1 28.3 + - + +
165A GLU* 1.3 79.5 - - - +
167A ALA* 1.3 57.6 + - - +
169A TRP* 3.2 16.2 + - + +
170A ALA* 3.0 26.5 + - - +
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Residues in contact with ALA 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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158A ALA* 4.9 1.7 - - + +
161A PHE* 3.6 37.9 - - + -
163A HIS 3.1 8.3 + - - +
164A VAL* 3.7 11.2 - - - +
165A GLU 3.2 0.2 - - - -
166A GLU* 1.3 75.2 - - - +
168A VAL* 1.3 60.2 + - - +
170A ALA* 3.3 3.8 + - - +
171A VAL* 2.9 33.1 + - + +
183A ALA* 5.9 1.3 - - + -
184A THR 5.9 0.2 - - - +
185A MET* 4.4 7.4 - - + -
205A LEU* 3.7 17.3 - - + -
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Residues in contact with VAL 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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164A VAL* 2.8 21.8 + - + +
165A GLU* 3.7 6.7 - - - +
167A ALA* 1.3 73.8 - - - +
169A TRP* 1.3 69.1 + - + +
171A VAL* 3.3 5.1 + - - +
172A GLU* 3.0 44.0 + - - +
204A ARG* 3.6 42.6 - - + +
205A LEU* 4.0 10.8 - - + -
208A ALA* 3.8 11.2 - - + -
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Residues in contact with TRP 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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132A LYS 4.7 5.2 - - - -
133A SER 4.4 1.3 - - - -
134A GLU* 3.4 57.6 + - + -
137A VAL* 4.2 24.9 - - + -
138A LYS* 3.7 23.8 - - + +
141A PHE* 4.1 6.5 - - + -
165A GLU* 3.1 46.4 + - + +
166A GLU* 3.4 22.9 - - + +
167A ALA 3.2 0.2 - - - -
168A VAL* 1.3 78.6 - - + +
170A ALA* 1.3 66.1 + - - +
172A GLU* 3.1 20.5 + - - +
173A THR* 3.0 26.3 + - - -
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Residues in contact with ALA 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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122A VAL* 5.3 1.6 - - + -
141A PHE* 3.4 24.1 - - + -
158A ALA* 3.9 13.0 - - + -
161A PHE* 3.6 30.1 - - + -
166A GLU 3.0 7.4 + - - +
167A ALA 3.4 8.5 - - - +
169A TRP* 1.3 78.1 - - - +
171A VAL* 1.3 57.2 + - - +
173A THR* 3.2 2.3 + - - -
174A LEU* 2.9 37.5 + - + +
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Residues in contact with VAL 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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158A ALA* 4.5 5.4 - - + -
167A ALA 2.9 21.8 + - - +
168A VAL 3.8 4.5 - - - +
169A TRP 3.2 0.2 - - - -
170A ALA* 1.3 74.6 - - - +
172A GLU* 1.3 57.8 + - - +
174A LEU* 4.5 5.4 - - - +
175A ILE* 3.0 33.3 + - + +
181A VAL* 4.3 12.3 - - + -
183A ALA* 3.8 28.5 - - + -
205A LEU* 4.1 9.0 - - + +
208A ALA* 3.5 32.1 - - + +
209A GLY 4.1 2.5 - - - -
210A ALA* 3.8 18.6 - - + +
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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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134A GLU* 4.1 1.9 - - - +
138A LYS* 2.6 37.2 + - - +
168A VAL* 3.0 35.2 + - + +
169A TRP* 3.5 15.2 - - - +
171A VAL* 1.3 73.4 - - - +
173A THR* 1.3 64.8 + - - +
175A ILE* 3.2 23.8 - - + +
176A ALA* 4.0 6.2 + - - +
208A ALA* 4.4 13.3 - - + +
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Residues in contact with THR 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* 3.3 30.3 - - + +
141A PHE* 3.8 26.4 - - + +
142A LEU* 3.5 34.5 - - + +
145A LEU* 3.9 10.8 - - + +
169A TRP 3.0 13.7 + - - -
170A ALA 3.5 7.4 - - - -
172A GLU* 1.3 77.2 - - - +
174A LEU* 1.3 63.2 + - + +
176A ALA* 3.4 19.4 - - - +
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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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122A VAL* 4.1 28.7 - - + -
141A PHE* 5.0 6.3 - - + +
145A LEU* 4.1 31.2 - - + -
156A LEU* 3.7 21.1 - - + +
157A ILE 4.5 0.7 - - - -
158A ALA* 4.1 30.1 - - + +
170A ALA* 2.9 21.7 + - + +
171A VAL 4.0 1.6 - - - +
172A GLU 3.3 0.2 - - - -
173A THR* 1.3 75.5 - - + +
175A ILE* 1.3 60.7 + - - +
176A ALA 3.1 2.0 - - - -
177A SER* 2.8 33.3 + - - -
181A VAL* 3.8 25.8 - - + -
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Residues in contact with ILE 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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171A VAL* 3.0 21.4 + - + +
172A GLU* 3.2 19.3 - - + +
174A LEU* 1.3 76.4 - - - +
176A ALA* 1.3 55.2 + - + +
177A SER* 3.0 1.3 - - - -
178A GLY* 3.0 21.1 + - - -
179A LYS 4.6 3.7 - - - +
181A VAL* 3.8 18.2 - - + -
208A ALA 3.3 19.3 - - - +
209A GLY* 3.6 31.6 - - - +
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Residues in contact with ALA 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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142A LEU* 6.3 2.0 - - + -
145A LEU* 5.3 2.7 - - + -
172A GLU 4.4 5.4 - - - +
173A THR* 3.4 15.7 + - - +
174A LEU 3.1 0.6 - - - -
175A ILE* 1.3 81.1 - - - +
177A SER* 1.3 60.0 + - - +
178A GLY 3.2 0.8 + - - -
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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