Contacts of the helix formed by residues 160 - 169 (chain G) in PDB entry 1MFR
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 GLY 160 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158G GLU 3.2 7.4 + - - -
159G ASN* 1.3 72.3 + - - +
161G MET* 1.3 64.0 + - - +
163G GLU* 3.3 6.0 + - - -
164G TYR* 3.1 18.5 + - - +
153H ARG* 3.3 43.3 + - - +
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Residues in contact with MET 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B MET* 3.6 29.2 - - + +
159G ASN* 3.4 9.7 + - - +
160G GLY* 1.3 73.0 - - - +
162G GLY* 1.3 65.6 + - - +
164G TYR* 3.4 1.9 + - - +
165G LEU* 3.1 24.7 + - + +
153H ARG 3.6 3.8 + - - -
154H LEU* 4.1 26.0 - - + +
159H ASN* 3.8 26.2 - - - +
161H MET* 3.6 34.3 - - + +
162H GLY* 4.4 4.3 - - - -
165H LEU* 4.0 24.5 - - + -
161I MET* 6.3 0.2 - - - +
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Residues in contact with GLY 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B MET* 4.4 3.1 - - - -
154G LEU* 3.3 35.9 - - - +
156G LEU* 3.9 6.1 - - - -
159G ASN* 3.3 24.6 + - - +
160G GLY 3.2 0.8 - - - -
161G MET* 1.3 79.6 - - - +
163G GLU* 1.3 61.7 + - - +
165G LEU* 3.5 2.1 + - - +
166G PHE 3.1 17.3 + - - -
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Residues in contact with GLU 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 3.9 19.1 - - + +
47G VAL* 5.8 0.2 - - - +
91G ASN* 3.5 13.0 - - - +
92G THR* 2.8 45.6 + - + +
156G LEU* 3.5 28.4 - - + +
159G ASN 3.3 10.3 + - - +
160G GLY* 3.3 10.7 + - - +
162G GLY* 1.3 74.2 - - - +
164G TYR* 1.3 65.3 + - - +
166G PHE* 3.3 6.6 + - - +
167G ASP* 3.2 20.1 + - - +
153H ARG* 3.5 21.8 + - - +
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Residues in contact with TYR 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 4.6 2.2 - - - -
160G GLY 3.1 13.2 + - - +
161G MET 3.6 7.4 - - - +
163G GLU* 1.3 77.7 - - - +
165G LEU* 1.3 72.5 + - + +
167G ASP* 3.3 4.3 + - - -
168G LYS* 3.1 60.5 + - + +
150H ASN* 3.2 29.2 - - + -
153H ARG* 4.1 8.9 - - - +
154H LEU* 3.8 41.5 - - + -
165H LEU* 4.4 7.6 - - + -
166H PHE* 3.5 8.8 - + - -
169H HIS* 3.1 31.5 - + + +
170H SER* 2.9 30.7 + - - -
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Residues in contact with LEU 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B MET* 3.9 27.1 - - + -
164B TYR* 4.2 9.4 - - + -
165B LEU* 4.0 26.2 - - + -
154G LEU* 4.9 2.9 - - + -
161G MET* 3.1 25.7 + - + +
162G GLY* 3.8 5.4 - - - +
163G GLU 3.3 0.2 - - - -
164G TYR* 1.3 81.7 - - + +
166G PHE* 1.3 65.4 + - - +
168G LYS* 3.1 3.5 + - + +
169G HIS* 3.0 49.6 + - + +
165H LEU* 4.0 30.7 - - + -
169H HIS* 4.6 7.6 - - + +
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Residues in contact with PHE 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B TYR* 3.5 9.8 + + - -
47G VAL* 4.3 6.7 - - + -
92G THR* 3.8 23.8 - - + -
96G MET* 4.3 6.1 - - + -
147G PHE* 3.6 45.1 - + + -
150G ASN* 4.6 2.5 - - + -
151G LEU* 3.5 35.2 - - + -
154G LEU* 3.8 14.1 - - + +
162G GLY 3.1 14.0 + - - +
163G GLU 3.5 9.2 - - - +
164G TYR 3.3 0.2 - - - -
165G LEU* 1.3 76.5 - - - +
167G ASP* 1.3 64.7 + - - +
170G SER* 3.0 47.3 + - - -
171G VAL* 3.8 20.2 + - + -
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Residues in contact with ASP 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 3.3 27.5 - - + +
45G HIS* 4.4 2.4 + - - +
46G ASN* 3.0 66.0 + - - +
47G VAL* 3.1 23.7 + - + +
163G GLU 3.2 9.1 + - - +
164G TYR 3.4 10.1 - - - +
165G LEU 3.2 0.2 - - - -
166G PHE* 1.3 83.0 - - - +
168G LYS* 1.3 81.2 + - - +
169G HIS 3.6 0.2 + - - -
171G VAL* 4.4 7.7 + - - +
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Residues in contact with LYS 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 5.0 1.4 - - - +
46G ASN* 4.4 8.7 - - - +
164G TYR* 3.1 58.7 + - + +
165G LEU* 3.1 8.5 + - + +
167G ASP* 1.3 104.0 + - - +
169G HIS* 1.3 65.3 + - + +
171G VAL 5.3 1.8 - - - -
150H ASN* 4.8 2.8 + - - -
169H HIS* 3.9 50.4 + - + +
170H SER* 4.5 4.5 - - - +
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Residues in contact with HIS 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B TYR* 3.1 28.5 - + + +
165B LEU* 4.5 5.0 - - + +
168B LYS* 3.8 36.1 + - + +
169B HIS* 4.0 29.3 + + - -
165G LEU* 3.0 34.5 + - + +
167G ASP 3.4 0.2 - - - -
168G LYS* 1.3 84.2 + - + +
170G SER* 1.3 62.0 - - - +
171G VAL 3.5 3.3 - - - -
169H HIS* 4.1 25.2 + + - -
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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