Contacts of the helix formed by residues 210 - 221 (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 HIS 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A TYR* 3.6 9.6 - - - -
177A SER 2.8 20.5 + - - +
178A GLU* 3.6 33.9 + - + +
180A PHE* 3.8 15.2 - + + -
208A ARG* 4.5 8.1 - - + -
209A THR* 1.3 72.7 + - - +
211A THR* 1.4 61.5 + - - +
213A THR* 5.0 1.3 - - - -
214A GLY 3.0 16.6 + - - -
246A PHE 3.3 11.6 + - - -
247A GLY* 3.1 33.1 + - - -
248A ASP* 3.0 31.8 - - - +
249A PRO* 4.1 10.7 - - + +
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Residues in contact with THR 211 (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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138A LEU* 4.3 1.4 - - + +
176A TYR* 2.8 36.3 + - + +
209A THR* 3.2 9.6 + - - -
210A HIS* 1.4 73.2 - - - +
212A ALA* 1.4 57.2 + - - +
214A GLY* 3.3 1.4 + - - -
215A ILE* 3.0 33.2 + - + +
239A VAL* 4.4 11.2 - - + -
241A THR* 4.5 6.6 + - - -
243A GLY 4.7 2.1 + - - -
245A LYS* 4.1 10.7 + - - +
248A ASP* 3.4 0.8 + - - -
252A TYR* 3.3 27.3 + - + +
283A GLU* 4.8 0.3 + - - -
287A ILE* 4.1 16.8 - - + -
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Residues in contact with ALA 212 (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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211A THR* 1.4 76.2 - - - +
213A THR* 1.3 66.4 + - - +
215A ILE* 3.1 4.1 + - - +
216A ARG 3.0 18.2 + - - -
245A LYS* 3.6 11.7 - - + +
248A ASP* 2.9 10.0 + - - +
250A LEU* 3.5 22.4 - - + +
251A GLY 3.8 19.3 - - - +
252A TYR* 4.0 12.3 - - + -
255A VAL* 3.4 19.8 - - + +
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Residues in contact with THR 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A PHE* 3.4 32.8 - - + -
210A HIS* 4.0 2.0 - - + -
212A ALA* 1.3 75.7 - - - +
214A GLY* 1.4 64.2 + - - +
216A ARG* 3.1 3.9 + - + +
217A LYS* 2.9 39.0 + - + +
248A ASP* 2.6 32.7 + - - -
249A PRO* 4.3 7.1 - - - +
250A LEU* 3.5 23.6 - - + +
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Residues in contact with GLY 214 (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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138A LEU* 3.6 20.7 - - - +
174A MET* 4.1 0.2 - - - +
176A TYR* 4.6 1.8 - - - -
180A PHE* 3.6 20.0 - - - -
210A HIS 3.0 14.5 + - - -
211A THR 3.3 4.0 + - - -
212A ALA 3.2 0.2 - - - -
213A THR* 1.4 77.1 - - - +
215A ILE* 1.3 56.1 + - - +
217A LYS* 3.2 3.8 + - - +
218A VAL* 2.9 32.4 + - - +
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Residues in contact with ILE 215 (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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138A LEU* 3.7 14.8 - - + +
211A THR* 3.0 25.5 + - + +
212A ALA 3.1 6.3 + - - +
214A GLY* 1.3 74.4 - - - +
216A ARG* 1.3 63.4 + - - +
218A VAL* 3.2 6.3 + - - +
219A VAL* 3.0 32.6 + - + +
237A LEU* 4.5 17.0 - - + -
239A VAL* 4.6 2.0 - - + -
252A TYR* 4.1 26.2 - - + -
255A VAL* 4.0 16.2 - - + +
256A ILE* 4.3 11.7 - - + -
259A ALA* 4.5 12.6 - - + -
266A ARG* 4.9 3.1 - - - -
287A ILE* 4.1 22.7 - - + +
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Residues in contact with ARG 216 (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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212A ALA 3.0 6.8 + - - +
213A THR* 3.5 9.9 - - - +
215A ILE* 1.3 75.4 - - - +
217A LYS* 1.3 63.5 + - + +
219A VAL* 3.2 6.6 + - - +
220A ARG* 2.9 79.2 + - - +
250A LEU* 3.6 30.4 - - + +
254A ASP* 3.0 36.2 + - - +
255A VAL* 3.8 20.6 - - + +
258A GLU* 4.5 4.8 + - - +
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Residues in contact with LYS 217 (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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174A MET* 3.7 19.1 - - + +
180A PHE* 3.5 49.6 - - + -
213A THR* 2.9 31.4 + - + +
214A GLY 3.8 2.5 - - - +
216A ARG* 1.3 76.9 - - + +
218A VAL* 1.3 66.1 + - - +
220A ARG* 4.5 1.6 - - - +
221A GLU* 2.8 56.2 + - - +
222A LEU 3.4 0.9 + - - -
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Residues in contact with VAL 218 (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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136A ALA* 4.2 5.8 - - + -
138A LEU* 4.0 33.0 - - + -
174A MET* 4.3 3.1 - - - -
214A GLY 2.9 18.6 + - - +
215A ILE 3.2 7.8 + - - +
217A LYS* 1.3 77.1 - - - +
219A VAL* 1.3 65.2 + - + +
222A LEU* 3.1 39.3 + - + +
223A PHE* 3.1 35.3 + - + -
237A LEU* 3.9 25.1 - - + -
264A VAL* 5.3 0.2 - - + -
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Residues in contact with VAL 219 (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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215A ILE* 3.0 21.3 + - + +
216A ARG* 3.2 6.7 + - - +
218A VAL* 1.3 83.5 - - + +
220A ARG* 1.3 61.2 + - - +
223A PHE* 3.6 24.9 - - - +
237A LEU* 5.8 0.2 - - + -
255A VAL 5.3 1.3 - - - +
258A GLU* 4.1 23.8 - - + +
259A ALA* 3.8 27.6 - - + +
262A GLU* 3.9 32.4 - - + +
264A VAL* 4.2 14.1 - - + -
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Residues in contact with ARG 220 (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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216A ARG* 2.9 63.5 + - + +
217A LYS* 4.6 1.1 - - - +
219A VAL* 1.3 79.1 - - + +
221A GLU* 1.3 65.7 + - + +
224A ASN* 3.0 28.1 + - - +
258A GLU* 2.8 43.8 + - - +
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Residues in contact with GLU 221 (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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174A MET* 3.9 11.1 - - + +
182A ILE* 3.6 26.7 - - + +
217A LYS* 2.8 47.5 + - - +
220A ARG* 1.3 82.7 - - + +
222A LEU* 1.3 67.4 + - - +
223A PHE 3.3 1.1 - - - -
224A ASN* 3.2 12.8 - - - +
227A ASN* 2.9 23.5 - - - +
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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