Contacts of the helix formed by residues 144 - 160 (chain L) in PDB entry 5MQF
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 MET 144 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143L ASP* 1.3 76.4 - - - +
145L ASP* 1.3 60.2 + - - +
147L ASP* 3.8 6.2 - - - +
148L GLU* 2.9 30.5 + - - +
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Residues in contact with ASP 145 (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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143L ASP 3.3 4.7 - - - +
144L MET* 1.3 79.3 - - - +
146L GLU* 1.3 57.8 + - - +
148L GLU* 3.4 5.5 + - - +
149L LEU* 2.9 28.3 + - - +
184O PRO* 6.4 2.0 - - + -
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Residues in contact with GLU 146 (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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143L ASP* 3.5 15.8 + - - +
145L ASP* 1.3 76.0 - - - +
147L ASP* 1.3 60.1 + - - +
149L LEU* 3.3 6.5 + - - +
150L GLU* 2.9 30.0 + - - +
149Y A 6.5 0.7 - - + -
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Residues in contact with ASP 147 (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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143L ASP 3.1 18.3 + - - +
144L MET* 3.9 6.7 - - - +
145L ASP 3.3 0.2 - - - -
146L GLU* 1.3 78.1 - - - +
148L GLU* 1.3 57.0 + - - +
150L GLU* 3.4 5.4 + - - +
151L MET* 2.9 29.3 + - - +
149Y A 6.4 1.6 - - + -
150Y U 4.8 14.1 - - - +
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Residues in contact with GLU 148 (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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14L THR* 5.6 10.3 - - - -
144L MET 2.9 18.3 + - - +
145L ASP* 3.8 6.1 - - - +
147L ASP* 1.3 73.6 - - - +
149L LEU* 1.3 59.5 - - - +
151L MET* 3.5 6.7 + - - +
152L LEU* 2.9 28.8 + - - +
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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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145L ASP 2.9 18.5 + - - +
146L GLU* 3.7 8.1 - - - +
147L ASP 3.3 0.2 - - - -
148L GLU* 1.3 75.7 - - - +
150L GLU* 1.3 60.0 + - - +
152L LEU* 3.3 6.2 + - - +
153L SER* 2.9 29.5 + - - -
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Residues in contact with GLU 150 (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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146L GLU 2.9 17.4 + - - +
147L ASP* 3.9 5.8 - - - +
148L GLU 3.4 0.2 - - - -
149L LEU* 1.3 76.8 - - - +
151L MET* 1.3 58.7 + - - +
153L SER* 3.4 5.7 + - - -
154L GLU* 2.9 31.2 + - - +
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Residues in contact with MET 151 (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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37L LEU 5.0 12.5 - - - +
39L HIS* 6.4 2.7 - - + -
147L ASP 2.9 19.1 + - - +
148L GLU* 3.8 7.9 - - - +
149L LEU 3.3 0.2 - - - -
150L GLU* 1.3 76.6 - - - +
152L LEU* 1.3 57.2 + - - +
154L GLU* 3.8 5.3 - - - +
155L ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 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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18L ILE* 4.4 22.4 - - + -
37L LEU 5.8 1.8 - - - -
148L GLU 2.9 18.4 + - - +
149L LEU* 3.6 7.4 - - - +
151L MET* 1.3 75.0 - - - +
153L SER* 1.3 58.9 + - - +
155L ALA* 3.1 7.6 + - - +
156L ARG* 2.9 29.3 + - - +
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Residues in contact with SER 153 (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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149L LEU 2.9 17.3 + - - -
150L GLU* 3.9 6.3 - - - -
152L LEU* 1.3 76.6 - - - +
154L GLU* 1.3 57.1 + - - +
156L ARG* 3.4 5.4 + - - +
157L ALA* 2.9 29.7 + - - +
195O LEU* 5.3 15.5 - - - -
199O LYS* 4.6 10.2 - - - +
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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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150L GLU 2.9 17.9 + - - +
151L MET* 4.1 5.6 - - - +
153L SER* 1.3 75.7 - - - +
155L ALA* 1.3 57.4 + - - +
157L ALA* 4.0 6.6 - - - +
158L ARG* 2.9 29.2 + - - +
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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
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496 G 5.9 0.4 - - - +
37L LEU* 4.5 22.0 - - + +
151L MET 2.9 20.4 + - - +
152L LEU* 3.1 10.2 + - - +
154L GLU* 1.3 76.1 - - - +
156L ARG* 1.3 60.3 + - - +
158L ARG* 3.3 7.5 + - - +
159L LEU* 2.9 24.1 + - - +
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Residues in contact with ARG 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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21L ALA* 6.3 3.1 - - + -
152L LEU 2.9 15.8 + - - +
153L SER* 4.0 5.4 - - - +
155L ALA* 1.3 73.6 - - - +
157L ALA* 1.3 60.3 + - - +
159L LEU* 3.0 10.6 + - - +
160L ALA* 2.9 26.5 + - - +
192O GLU 5.9 0.4 - - - +
195O LEU* 5.8 1.3 - - + -
196O ARG* 4.7 24.9 - - + +
199O LYS* 5.4 2.5 - - + -
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Residues in contact with ALA 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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153L SER 2.9 19.0 + - - +
154L GLU* 4.0 7.4 - - - +
156L ARG* 1.3 76.0 - - - +
158L ARG* 1.3 57.9 + - - +
160L ALA* 3.3 8.3 + - - +
161L ASN* 2.9 26.3 + - - +
199O LYS* 4.3 22.1 - - + +
203O LEU* 5.8 2.4 - - + +
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Residues in contact with ARG 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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486 A 4.0 8.6 + - - +
496 G 4.1 27.2 - - - +
154L GLU 2.9 20.5 + - - +
155L ALA* 3.5 8.3 - - - +
156L ARG 3.2 0.2 - - - -
157L ALA* 1.3 73.8 - - - +
159L LEU* 1.3 61.9 + - - +
161L ASN* 3.0 23.6 + - + +
162L THR* 3.3 9.0 + - - -
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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
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486 A 4.0 11.3 + - - +
260C TYR* 4.2 18.7 - - + +
25L LYS* 4.4 22.7 - - + -
155L ALA 2.9 14.0 + - - +
156L ARG* 3.0 13.2 + - - +
158L ARG* 1.3 76.8 - - - +
160L ALA* 1.3 59.9 + - - +
162L THR* 3.4 19.8 - - - -
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Residues in contact with ALA 160 (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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260C TYR* 5.7 1.1 - - - -
156L ARG 2.9 12.8 + - - +
157L ALA* 3.5 10.5 - - - +
159L LEU* 1.3 75.7 - - - +
161L ASN* 1.3 55.9 + - - +
162L THR* 3.3 2.8 + - - -
163L GLN* 4.8 3.3 + - - +
199O LYS 5.6 0.4 - - - +
200O GLU* 5.2 11.2 - - + -
203O LEU* 4.4 24.2 - - + +
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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