Contacts of the helix formed by residues 148 - 166 (chain L) in PDB entry 3MQT
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 THR 148 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C GLU* 4.5 10.1 + - - +
146L ASP 4.8 4.5 - - - +
147L ALA* 1.3 76.0 - - - +
149L LEU* 1.3 64.9 + - - +
150L SER* 3.6 9.6 + - - -
151L GLU* 3.0 38.3 + - - +
152L ILE* 2.9 25.4 + - - +
178L ASN* 5.7 0.7 - - - +
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Residues in contact with LEU 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L ALA 4.1 0.4 + - - -
148L THR* 1.3 71.8 - - - +
150L SER* 1.3 63.4 + - - +
152L ILE* 3.1 16.3 + - + +
153L VAL* 2.9 28.7 + - - +
175L ILE* 5.7 2.0 - - + -
176L ILE 5.9 1.3 - - - +
178L ASN* 5.0 9.6 - - + +
181L VAL* 3.9 33.4 - - + -
185L GLU* 3.8 35.0 - - + +
186L ILE* 4.4 13.7 - - + -
189L TYR* 3.9 33.1 - - + -
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Residues in contact with SER 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C SER* 2.6 28.8 + - - -
154C GLU* 3.5 36.0 + - - +
157C LYS* 5.3 2.9 - - - -
192C GLU* 5.0 5.4 + - - -
148L THR* 3.2 5.1 + - - -
149L LEU* 1.3 79.7 - - - +
151L GLU* 1.3 63.7 + - - +
153L VAL* 3.3 8.7 + - - +
154L GLU* 3.0 24.8 + - - +
192L GLU* 5.3 7.3 + - - -
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Residues in contact with GLU 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C GLU* 5.9 4.0 - - + -
143L VAL* 4.5 4.3 - - + +
147L ALA* 3.6 15.2 - - + +
148L THR* 3.0 39.5 + - - +
150L SER* 1.3 77.4 - - - +
152L ILE* 1.3 58.1 + - - +
154L GLU* 3.2 9.1 + - - +
155L ALA* 2.8 29.0 + - - +
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Residues in contact with ILE 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L PRO* 4.0 11.4 - - + -
143L VAL* 4.3 11.4 - - + -
147L ALA* 3.9 28.0 - - + +
148L THR 2.9 22.1 + - - +
149L LEU* 3.6 19.7 - - + +
151L GLU* 1.3 76.0 - - - +
153L VAL* 1.3 51.5 + - - +
155L ALA* 3.0 9.9 + - - +
156L TYR* 2.7 46.6 + - + -
176L ILE* 4.3 28.0 - - + +
178L ASN* 5.7 2.7 - - - +
189L TYR* 3.3 26.2 - - + +
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Residues in contact with VAL 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L LEU 2.9 19.2 + - - +
150L SER* 3.5 8.7 - - - +
152L ILE* 1.3 75.4 - - - +
154L GLU* 1.3 69.5 + - - +
156L TYR* 3.0 19.7 + - - +
157L LYS* 3.1 15.8 + - - +
189L TYR* 3.6 26.7 - - + +
192L GLU* 3.5 44.2 - - + +
193L LEU* 4.4 13.7 - - + -
196L VAL* 4.5 15.3 - - + -
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Residues in contact with GLU 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C THR* 4.5 13.9 + - - +
150C SER* 3.4 31.8 + - - +
151C GLU* 6.1 2.9 - - + -
150L SER 3.0 17.8 + - - +
151L GLU* 3.6 11.2 - - - +
153L VAL* 1.3 82.0 - - - +
155L ALA* 1.3 60.9 + - - +
157L LYS* 2.7 43.3 + - - +
158L PRO* 3.3 18.9 - - - +
192L GLU* 4.3 2.4 - - - +
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Residues in contact with ALA 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141L PRO* 3.8 13.6 - - + +
142L SER 4.5 4.7 - - - +
143L VAL* 3.5 31.0 - - + -
151L GLU 2.8 8.7 + - - +
152L ILE 3.4 7.4 - - - +
154L GLU* 1.3 73.6 - - - +
156L TYR* 1.3 65.3 + - - +
158L PRO* 3.3 16.6 - - - +
159L LEU* 4.2 10.7 + - - +
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Residues in contact with TYR 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L LEU* 2.7 48.8 + - + -
141L PRO* 3.5 27.3 - - + +
152L ILE* 2.7 30.1 + - + -
153L VAL 3.0 10.9 + - - +
155L ALA* 1.3 74.5 - - - +
157L LYS* 1.3 61.8 + - + +
159L LEU* 3.1 12.2 + - + +
160L ILE* 2.9 33.0 + - + +
173L VAL* 3.7 22.4 - - + -
174L CYS* 2.9 23.6 + - - +
176L ILE* 6.1 0.2 - - + -
189L TYR* 3.5 20.2 - - - -
193L LEU* 3.8 25.1 - - + -
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Residues in contact with LYS 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C SER* 5.0 3.2 - - - -
153L VAL* 3.1 17.5 + - - +
154L GLU* 2.7 47.6 + - - +
155L ALA 3.3 0.2 - - - -
156L TYR* 1.3 75.2 - - - +
158L PRO* 1.3 66.4 - - + +
160L ILE* 3.9 1.1 - - - +
161L ALA* 3.0 30.3 + - - +
192L GLU* 4.5 7.8 + - - -
196L VAL* 4.0 39.5 - - + +
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Residues in contact with PRO 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L GLU 3.3 11.9 - - - +
155L ALA* 3.3 15.9 - - - +
157L LYS* 1.3 92.9 - - + +
159L LEU* 1.3 56.1 + - + +
161L ALA* 3.5 7.3 + - + +
162L LYS* 2.9 37.5 + - - +
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Residues in contact with LEU 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139L LEU* 4.4 18.3 - - + +
140L TYR 3.8 31.0 - - - +
141L PRO* 3.9 19.5 - - + -
142L SER 5.3 0.2 - - - +
155L ALA 4.4 8.7 - - - +
156L TYR* 3.1 10.4 + - + +
158L PRO* 1.3 76.9 - - + +
160L ILE* 1.3 60.2 + - - +
162L LYS* 3.1 12.3 + - - +
163L ALA* 2.9 26.5 + - - +
339L ASP 4.7 3.4 - - - +
340L PHE* 3.5 46.1 - - + +
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Residues in contact with ILE 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139L LEU* 3.7 24.0 - - + -
156L TYR* 2.9 36.4 + - + +
157L LYS 4.0 3.1 - - - +
159L LEU* 1.3 73.8 - - - +
161L ALA* 1.3 62.7 + - - +
163L ALA* 3.1 6.1 + - - +
164L LYS* 3.0 31.5 + - - +
171L VAL* 5.1 0.4 - - + -
173L VAL* 4.8 1.1 - - + -
193L LEU* 4.4 8.1 - - + -
196L VAL* 3.8 29.8 - - + +
197L ILE* 3.6 47.3 - - + -
201L MET* 4.2 5.6 - - + -
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Residues in contact with ALA 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L LYS 3.0 18.8 + - - +
158L PRO* 3.7 7.4 - - + +
160L ILE* 1.3 76.4 - - - +
162L LYS* 1.3 58.3 + - - +
164L LYS* 3.4 11.5 + - - +
165L GLU* 3.0 26.4 + - - +
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Residues in contact with LYS 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158L PRO* 2.9 30.4 + - - +
159L LEU* 3.1 12.0 + - + +
161L ALA* 1.3 74.3 - - - +
163L ALA* 1.3 64.2 + - - +
165L GLU* 3.2 4.4 + - - -
166L ARG* 2.8 68.6 + - - +
339L ASP* 3.4 30.8 + - + +
340L PHE* 3.9 7.4 - - + -
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Residues in contact with ALA 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L LEU* 4.7 1.8 - - + -
159L LEU 2.9 12.8 + - - +
160L ILE* 3.4 11.7 - - - +
162L LYS* 1.3 74.8 - - - +
164L LYS* 1.3 63.9 + - - +
166L ARG* 3.1 9.4 + - - +
167L GLY 3.2 0.2 + - - -
168L ALA* 3.1 30.8 + - + +
171L VAL* 3.7 30.3 - - + -
201L MET* 4.4 3.4 - - + -
340L PHE* 3.6 21.6 - - + -
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Residues in contact with LYS 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160L ILE* 3.0 24.1 + - + +
161L ALA* 3.6 12.1 - - - +
163L ALA* 1.3 76.5 - - - +
165L GLU* 1.3 59.1 + - - +
167L GLY* 2.9 19.6 + - - +
168L ALA 4.7 1.1 - - - +
196L VAL 2.9 24.5 + - - -
197L ILE 3.1 26.6 + - - -
198L GLY* 4.5 2.0 - - - +
201L MET* 3.8 20.6 - - + -
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Residues in contact with GLU 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161L ALA 3.0 13.8 + - - +
162L LYS* 3.2 11.2 + - - +
164L LYS* 1.3 76.0 - - - +
166L ARG* 1.3 84.2 + - - +
167L GLY 3.3 1.2 + - - -
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Residues in contact with ARG 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L LYS* 2.8 55.9 + - - +
163L ALA* 3.1 9.8 + - - +
165L GLU* 1.3 100.4 + - - +
167L GLY* 1.3 57.5 + - - +
168L ALA* 4.6 1.3 - - + +
339L ASP* 3.0 28.1 + - - +
340L PHE* 4.5 4.0 - - + -
355L LYS* 2.8 37.3 - - - +
356L ILE* 3.7 33.3 - - + +
358L ASP* 3.3 10.7 + - - -
359L GLY 3.0 19.9 + - - -
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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
------------------------------------------------------------
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