Contacts of the helix formed by residues 185 - 192 (chain A) in PDB entry 1MF7
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A PHE 3.7 5.3 - - - +
172A SER* 3.5 6.7 - - - -
182A ILE* 3.8 21.3 - - + -
184A PHE* 1.3 76.9 - - - +
186A PHE* 1.3 67.5 + - - +
187A LYS* 3.6 4.0 + - - +
188A GLU* 2.9 37.6 + - - +
189A PHE* 2.9 19.1 + - - +
222A LEU* 5.1 2.2 - - + -
227A ASN* 3.4 42.6 - - + +
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Residues in contact with PHE 186 (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 ASP* 3.6 18.8 - - + -
135A ILE 3.4 36.8 - - - -
136A ALA* 4.0 2.7 - - + -
170A LEU* 3.5 25.0 - - + +
171A PHE 3.4 16.8 - - - -
172A SER* 3.5 18.6 - - - -
185A THR* 1.3 74.3 - - - +
187A LYS* 1.3 56.8 + - - +
189A PHE* 3.3 3.1 + - - +
190A GLN* 2.9 29.1 + - - +
222A LEU* 3.3 29.8 + - + -
223A PHE* 3.6 28.0 - + - -
227A ASN* 3.2 6.9 + - - +
228A GLY* 3.7 14.4 - - - +
229A ALA* 3.9 15.3 - - + -
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Residues in contact with LYS 187 (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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185A THR* 3.2 4.9 - - - +
186A PHE* 1.3 75.3 - - - +
188A GLU* 1.3 62.5 + - + +
190A GLN* 3.2 13.2 + - + +
191A ASN* 3.1 35.8 + - - +
225A ILE 5.1 1.5 + - - -
226A THR* 3.1 29.3 + - - +
227A ASN* 2.9 13.8 + - - +
228A GLY* 3.8 15.2 - - - +
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Residues in contact with GLU 188 (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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182A ILE* 5.0 1.9 - - - +
183A HIS 4.1 4.3 - - - +
184A PHE* 3.2 18.4 - - + -
185A THR* 2.9 40.7 + - - +
187A LYS* 1.3 76.0 - - + +
189A PHE* 1.3 64.0 + - - +
191A ASN* 3.2 7.5 + - - +
192A ASN* 3.0 24.3 + - - +
198A LEU* 5.1 5.2 - - + +
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Residues in contact with PHE 189 (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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161A MET* 3.7 20.9 - - + -
165A LYS* 4.3 11.4 - - + -
169A THR 4.1 12.8 - - - -
170A LEU* 3.9 11.9 - - + -
171A PHE* 3.1 60.1 - + + +
184A PHE* 4.2 5.3 - + + -
185A THR 2.9 7.7 + - - +
186A PHE 3.6 4.7 - - - +
188A GLU* 1.3 77.5 - - - +
190A GLN* 1.3 64.9 + - - +
192A ASN 4.1 3.4 - - - -
193A PRO* 2.9 68.4 - - + +
194A ASN 3.9 2.7 - - - -
195A PRO* 3.9 9.0 - - + -
198A LEU* 3.7 19.5 - - + -
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Residues in contact with GLN 190 (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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170A LEU* 3.7 34.6 - - + +
186A PHE 2.9 16.4 + - - +
187A LYS* 3.2 12.7 + - - +
189A PHE* 1.3 79.5 - - - +
191A ASN* 1.3 71.6 + - - +
193A PRO* 3.8 12.0 - - - +
228A GLY* 5.2 1.7 - - - +
230A ARG* 5.2 4.2 - - - +
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Residues in contact with ASN 191 (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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187A LYS* 3.1 30.4 + - - +
188A GLU* 3.2 6.2 + - - +
189A PHE 3.1 1.0 - - - -
190A GLN* 1.3 93.2 + - - +
192A ASN* 1.3 58.8 + - + +
193A PRO* 3.8 3.3 - - - +
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Residues in contact with ASN 192 (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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188A GLU 3.0 11.5 + - - +
189A PHE* 3.0 5.4 + - - +
191A ASN* 1.3 79.1 - - + +
193A PRO* 1.3 52.7 - - - +
194A ASN* 2.7 47.4 + - - +
197A SER* 3.8 18.1 + - - -
198A LEU* 3.4 31.1 - - + +
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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