Contacts of the helix formed by residues 214 - 226 (chain A) in PDB entry 5MQI
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 TRP 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LEU* 5.1 0.2 - - - +
148A ARG* 4.3 4.9 - - - +
153A ASN* 3.3 35.9 - - + -
156A ILE* 3.6 26.0 - - + +
157A GLU* 3.5 31.6 - - + -
160A LEU* 4.1 22.9 - - + -
205A LEU* 4.1 11.7 - - + -
211A GLU* 3.0 41.0 + - + +
213A GLN* 1.3 114.0 + - + +
215A SER* 1.3 58.2 + - - +
216A LEU 3.3 2.7 - - - -
217A HIS* 3.2 21.5 + + - +
218A VAL* 2.9 34.9 + - + +
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Residues in contact with SER 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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205A LEU 6.1 0.4 - - - -
211A GLU 4.0 1.0 + - - -
212A GLU* 3.3 8.9 + - - -
213A GLN 3.4 1.0 - - - -
214A TRP* 1.3 77.1 - - - +
216A LEU* 1.4 59.7 + - - +
218A VAL* 4.5 2.2 - - - +
219A LEU* 2.9 27.9 + - - +
357A LEU* 3.4 28.6 - - - +
360A SER* 2.8 35.2 + - - -
361A VAL* 3.6 6.2 + - - +
364A HIS* 3.1 17.8 - - - -
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Residues in contact with LEU 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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213A GLN 5.1 1.4 + - - -
214A TRP 3.3 0.4 - - - -
215A SER* 1.4 81.5 + - - +
217A HIS* 1.3 72.6 + - + +
219A LEU* 3.4 3.1 + - - +
220A GLU* 3.0 32.7 + - + +
361A VAL* 3.7 31.0 - - + -
364A HIS* 4.2 27.5 - - + +
365A LEU* 4.2 13.0 - - + -
368A GLU* 4.7 0.9 - - - +
373A HIS* 3.5 46.9 - - + +
374A ASP 5.4 4.0 - - - +
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Residues in contact with HIS 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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157A GLU* 4.1 24.3 + - + +
160A LEU* 4.1 25.8 - - + -
161A LEU* 3.7 31.1 - - + +
164A ARG* 5.1 4.6 - - + +
213A GLN 4.3 6.1 + - - -
214A TRP* 3.2 36.8 + + - +
216A LEU* 1.3 83.9 - - + +
218A VAL* 1.3 61.9 + - - +
220A GLU* 3.3 8.2 + - - +
221A ILE* 3.1 29.6 + - + +
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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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160A LEU* 4.8 4.9 - - + -
202A LEU* 3.8 29.8 - - + +
205A LEU* 3.7 36.3 - - + -
206A ALA* 4.2 13.5 - - + -
214A TRP* 2.9 27.6 + - + +
215A SER* 4.0 3.8 - - - +
217A HIS* 1.3 76.6 - - - +
219A LEU* 1.4 63.0 + - - +
221A ILE* 3.2 7.3 + - - +
222A VAL* 3.0 35.8 + - + +
357A LEU* 4.4 8.7 - - + -
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Residues in contact with LEU 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 SER 2.9 17.9 + - - +
216A LEU* 3.9 3.8 - - - +
218A VAL* 1.4 76.3 - - - +
220A GLU* 1.3 63.5 + - - +
222A VAL* 4.6 4.9 - - + +
223A SER* 2.9 35.5 + - - +
349A PHE* 4.6 8.5 - - + -
357A LEU* 3.7 25.2 - - + +
358A MET* 4.0 16.6 - - - -
361A VAL* 4.1 22.0 - - + -
377A TYR* 3.9 6.5 - - + +
378A TYR* 3.8 35.2 - - - +
381A ALA* 3.7 21.5 - - + -
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Residues in contact with GLU 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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164A ARG* 2.8 48.3 + - + -
216A LEU* 3.0 23.5 + - + +
217A HIS* 3.7 8.7 - - - +
218A VAL 3.2 0.2 - - - -
219A LEU* 1.3 76.5 - - - +
221A ILE* 1.3 64.3 + - - +
223A SER* 3.9 1.0 - - - -
224A LEU* 3.0 31.0 + - + +
374A ASP* 4.7 9.5 + - - +
377A TYR* 3.4 50.7 + - + -
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Residues in contact with ILE 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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160A LEU* 3.6 45.8 - - + +
163A VAL* 4.2 10.3 - - + -
164A ARG* 3.9 24.9 - - + +
167A LEU* 3.6 20.9 - - + +
193A ILE* 5.6 0.2 - - + -
202A LEU* 3.7 35.2 - - + -
217A HIS* 3.1 22.6 + - + +
218A VAL* 3.2 4.2 + - - +
220A GLU* 1.3 78.4 - - - +
222A VAL* 1.3 55.9 + - - +
224A LEU* 3.2 6.1 + - - +
225A MET* 2.9 30.0 + - - +
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Residues in contact with VAL 222 (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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202A LEU* 4.9 7.4 - - + +
218A VAL* 3.0 34.1 + - + +
219A LEU* 4.0 5.4 - - + +
221A ILE* 1.3 72.1 - - - +
223A SER* 1.4 68.3 + - - +
225A MET* 3.1 14.9 + - - +
226A PHE* 3.1 25.2 - - + -
345A PHE* 4.2 33.7 - - + -
349A PHE* 4.2 23.6 - - + -
385A PHE* 3.8 26.7 - - + -
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Residues in contact with SER 223 (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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173A LEU* 4.0 4.9 - - - +
219A LEU* 2.9 21.8 + - - +
222A VAL* 1.4 78.9 - - - +
224A LEU* 1.3 63.0 + - - +
226A PHE* 3.2 12.5 + - - -
227A ARG* 3.4 8.8 + - - +
377A TYR* 3.8 27.4 + - - -
380A TRP* 3.8 29.5 - - - -
381A ALA* 3.9 22.7 - - - +
385A PHE* 5.1 1.2 - - - -
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Residues in contact with LEU 224 (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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164A ARG* 3.8 33.7 - - + +
167A LEU* 3.8 16.4 - - + +
168A HIS* 4.0 18.2 - - + +
171A ALA 4.9 0.9 - - - +
173A LEU* 4.0 26.9 - - + +
186A HIS* 2.8 29.1 + - - -
220A GLU 3.0 26.2 + - - +
221A ILE* 3.2 4.5 + - - +
223A SER* 1.3 75.1 - - - +
225A MET* 1.3 55.5 - - - +
226A PHE 3.3 0.5 + - - -
227A ARG* 3.3 30.7 + - - +
377A TYR* 4.1 20.4 - - + +
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Residues in contact with MET 225 (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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167A LEU* 4.2 12.8 - - + -
186A HIS* 3.9 4.4 + - - -
190A LEU* 3.6 42.0 - - + +
193A ILE* 4.3 14.4 - - + -
202A LEU* 3.9 25.6 - - - -
221A ILE* 2.9 20.5 + - - +
222A VAL* 3.1 16.3 + - - +
224A LEU* 1.3 76.7 - - - +
226A PHE* 1.3 63.2 + - + +
227A ARG 3.4 0.9 + - - -
228A ASP 5.0 0.5 + - - -
229A GLN* 4.9 1.0 + - - +
341A PHE* 3.9 32.3 - - + -
342A LEU* 3.9 9.8 - - + +
345A PHE* 4.1 27.6 - - + -
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Residues in contact with PHE 226 (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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222A VAL* 3.1 22.0 - - + +
223A SER 3.2 4.9 + - - +
224A LEU 3.1 1.2 - - - -
225A MET* 1.3 79.6 - - + +
227A ARG* 1.3 64.9 + - - +
228A ASP 3.2 2.2 - - - -
229A GLN* 3.1 25.1 + - + +
234A LEU* 3.7 18.6 - - + -
342A LEU* 3.5 43.7 - - + -
345A PHE* 3.6 34.1 - + - -
346A CYS* 3.7 14.8 - - + -
380A TRP* 3.7 24.9 - - + -
384A PHE* 3.6 24.9 - + + -
385A PHE* 4.0 17.0 - + - -
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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