Contacts of the helix formed by residues 148 - 166 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146S ASP 5.0 3.6 - - - +
147S ALA* 1.3 77.6 - - - +
149S LEU* 1.3 64.2 + - - +
150S SER* 3.5 9.0 + - - -
151S GLU* 3.1 41.2 + - - +
152S ILE* 3.0 22.2 + - - +
178S ASN* 5.9 0.4 - - - -
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Residues in contact with LEU 149 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148S THR* 1.3 74.6 - - - +
150S SER* 1.3 63.2 + - - +
152S ILE* 3.4 17.4 + - + +
153S VAL* 3.0 27.5 + - - +
175S ILE* 6.1 1.3 - - + -
176S ILE 6.0 0.9 - - - +
178S ASN* 5.0 10.1 + - + +
181S VAL* 3.9 33.0 - - + -
185S GLU* 3.9 31.0 - - + +
186S ILE* 4.2 14.6 - - + -
189S TYR* 3.9 34.0 - - + -
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Residues in contact with SER 150 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148S THR* 3.3 6.6 + - - -
149S LEU* 1.3 78.7 - - - +
151S GLU* 1.3 61.3 + - - +
153S VAL* 3.3 9.4 + - - +
154S GLU* 3.0 31.9 + - - +
192S GLU* 5.2 8.2 + - - -
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Residues in contact with GLU 151 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143S VAL* 4.6 4.0 - - + +
144S ALA* 5.9 0.7 - - - +
147S ALA* 3.6 17.0 - - + +
148S THR* 3.1 48.4 + - - +
150S SER* 1.3 76.5 - - - +
152S ILE* 1.3 58.6 + - - +
154S GLU* 3.1 11.0 + - + +
155S ALA* 3.0 26.3 + - - +
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Residues in contact with ILE 152 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141S PRO* 4.1 10.5 - - + +
143S VAL* 4.3 18.8 - - + -
147S ALA* 3.9 25.4 - - + +
148S THR 3.0 20.1 + - - +
149S LEU* 3.7 19.5 - - + +
151S GLU* 1.3 72.5 - - - +
153S VAL* 1.3 67.0 + - - +
155S ALA* 3.1 2.9 + - - +
156S TYR* 2.9 34.5 + - + -
176S ILE* 3.7 29.8 - - + +
178S ASN* 5.8 2.0 - - - +
189S TYR* 3.5 26.7 - - + +
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Residues in contact with VAL 153 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149S LEU 3.0 20.0 + - - +
150S SER* 3.3 9.8 + - - +
152S ILE* 1.3 75.3 - - - +
154S GLU* 1.3 65.7 + - - +
156S TYR* 3.1 17.4 + - - +
157S LYS* 3.2 28.5 + - - +
189S TYR* 3.7 26.0 - - + +
192S GLU* 3.4 39.3 - - + +
193S LEU* 4.2 18.6 - - + -
196S VAL* 4.5 7.1 - - + +
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Residues in contact with GLU 154 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150S SER* 3.0 25.1 + - - +
151S GLU* 3.1 12.3 + - + +
153S VAL* 1.3 79.1 - - - +
155S ALA* 1.3 60.6 + - - +
157S LYS* 3.3 46.0 + - - +
158S PRO* 3.4 10.7 - - - +
192S GLU* 5.3 1.6 - - - +
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Residues in contact with ALA 155 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141S PRO* 3.9 12.1 - - + -
142S SER 4.3 7.6 - - - +
143S VAL* 3.7 30.1 - - + -
151S GLU 3.0 8.7 + - - +
152S ILE 3.1 5.1 + - - +
154S GLU* 1.3 74.3 - - - +
156S TYR* 1.3 64.0 + - - +
157S LYS 3.5 0.2 + - - -
158S PRO* 3.5 15.6 - - - +
159S LEU* 3.9 13.2 - - - +
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Residues in contact with TYR 156 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139S LEU* 2.7 48.1 + - + -
141S PRO* 3.6 27.3 - - + +
152S ILE* 2.9 25.7 + - + -
153S VAL 3.1 9.4 + - - +
155S ALA* 1.3 77.4 - - - +
157S LYS* 1.3 64.6 + - - +
159S LEU* 3.0 12.5 + - + +
160S ILE* 2.9 39.5 + - + +
173S VAL* 3.9 16.4 - - + -
174S CYS* 2.9 25.1 + - - +
189S TYR* 3.4 22.9 - - - -
193S LEU* 4.0 22.7 - - + -
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Residues in contact with LYS 157 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200J ASP* 4.3 29.3 + - - -
153S VAL* 3.2 29.6 + - - +
154S GLU* 3.3 37.8 + - - +
156S TYR* 1.3 76.2 - - - +
158S PRO* 1.3 66.8 - - + +
160S ILE* 3.5 6.8 + - - +
161S ALA* 3.0 29.0 + - - +
192S GLU* 4.5 4.0 + - - -
196S VAL* 4.3 28.5 - - + +
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Residues in contact with PRO 158 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154S GLU 3.4 11.7 - - - +
155S ALA* 3.5 11.7 - - - +
157S LYS* 1.3 95.7 - - + +
159S LEU* 1.3 63.1 + - + +
161S ALA* 4.0 6.7 - - + +
162S LYS* 3.1 24.9 + - - +
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Residues in contact with LEU 159 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139S LEU* 4.1 17.4 - - + +
140S TYR 3.8 12.3 - - - +
141S PRO* 3.7 33.2 - - + -
142S SER 5.0 0.9 - - - +
155S ALA 3.9 13.2 - - - +
156S TYR* 3.0 13.7 + - + +
158S PRO* 1.3 80.7 - - + +
160S ILE* 1.3 56.9 + - - +
162S LYS* 3.3 8.5 + - + +
163S ALA* 3.1 27.7 + - - +
339S ASP 4.7 2.9 - - - +
340S PHE* 3.6 44.1 - - + +
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Residues in contact with ILE 160 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139S LEU* 3.9 21.1 - - + -
156S TYR* 2.9 39.0 + - + +
157S LYS 3.9 3.8 - - - +
159S LEU* 1.3 73.9 - - - +
161S ALA* 1.3 65.9 - - - +
163S ALA* 3.3 6.0 + - - +
164S LYS* 3.0 32.9 + - - +
171S VAL* 5.3 0.2 - - + -
173S VAL* 5.1 0.9 - - + -
193S LEU* 4.3 10.1 - - + -
196S VAL* 3.6 32.3 - - + +
197S ILE* 4.0 41.5 - - + -
201S MET* 4.4 5.6 - - + -
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Residues in contact with ALA 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161J ALA* 6.1 5.8 - - + +
164J LYS* 6.3 4.3 - - + -
157S LYS 3.0 18.3 + - - +
158S PRO* 4.0 7.6 - - + +
160S ILE* 1.3 78.2 - - - +
162S LYS* 1.3 58.5 + - - +
164S LYS* 3.3 11.8 + - - +
165S GLU* 3.0 28.1 + - - +
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Residues in contact with LYS 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158S PRO 3.1 19.7 + - - +
159S LEU* 3.7 7.0 - - + +
160S ILE 3.2 0.2 - - - -
161S ALA* 1.3 75.3 - - - +
163S ALA* 1.3 63.3 + - - +
165S GLU* 3.1 7.6 + - - +
166S ARG* 3.0 64.5 + - + +
339S ASP* 2.9 43.0 + - + +
340S PHE* 4.0 8.3 - - + -
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Residues in contact with ALA 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139S LEU* 4.7 2.0 - - + -
159S LEU 3.1 13.2 + - - +
160S ILE* 3.5 10.3 - - - +
162S LYS* 1.3 76.7 - - - +
164S LYS* 1.3 60.1 + - - +
166S ARG* 3.3 2.9 + - - +
167S GLY 3.2 4.2 + - - -
168S ALA* 2.9 35.8 + - + +
171S VAL* 3.8 28.7 - - + -
201S MET* 4.5 2.7 - - - -
340S PHE* 3.6 23.1 - - + -
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Residues in contact with LYS 164 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161J ALA* 6.5 0.9 - - + -
164J LYS* 3.7 20.6 - - - +
195J GLU 5.8 0.4 + - - -
196J VAL* 4.8 4.2 + - - +
160S ILE* 3.0 26.0 + - + +
161S ALA* 3.6 12.1 - - - +
163S ALA* 1.3 75.1 - - - +
165S GLU* 1.3 63.3 + - - +
167S GLY* 3.0 14.3 + - - -
168S ALA 4.9 0.7 - - - +
196S VAL 2.8 25.4 + - - -
197S ILE 3.0 24.2 + - - -
198S GLY* 4.5 2.2 - - - +
201S MET* 4.0 18.4 - - + -
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Residues in contact with GLU 165 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161S ALA 3.0 14.3 + - - +
162S LYS* 3.1 9.2 + - - +
164S LYS* 1.3 78.0 - - - +
166S ARG* 1.3 97.4 + - - +
167S GLY 3.5 0.5 + - - -
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Residues in contact with ARG 166 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162S LYS* 3.0 60.4 + - + +
163S ALA* 3.3 5.8 + - - +
164S LYS 3.2 0.2 - - - -
165S GLU* 1.3 109.5 + - - +
167S GLY* 1.3 58.6 + - - +
168S ALA* 3.5 0.8 + - - +
339S ASP* 3.2 24.9 + - - +
340S PHE* 4.8 2.7 - - + -
355S LYS* 3.2 32.9 - - - +
356S ILE* 3.6 42.2 - - + +
358S ASP 3.3 10.8 + - - -
359S GLY 2.9 19.6 + - - -
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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