Contacts of the helix formed by residues 252 - 261 (chain C) in PDB entry 1MPX
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 SER 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217C GLN* 4.8 1.3 - - - -
247C PHE* 5.9 0.2 - - - -
251C GLY* 1.3 77.6 + - - +
253C ALA* 1.3 63.8 + - - +
255C ASP* 3.1 28.8 + - - -
256C PHE* 3.2 21.0 + - - +
597C ASP* 6.0 0.2 - - - -
598C ARG* 4.7 0.2 - - - +
607C ILE 4.2 6.3 - - - -
608C PHE 3.1 20.7 + - - -
609C PHE* 4.4 1.6 - - - -
610C ALA 3.6 17.6 + - - -
615C TYR* 3.2 24.8 + - - -
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Residues in contact with ALA 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C PHE* 4.0 13.7 - - + -
217C GLN* 3.5 25.4 + - - +
220C PHE* 3.6 9.0 - - + -
252C SER* 1.3 74.7 - - - +
254C GLY* 1.3 57.1 + - - +
256C PHE* 3.3 3.4 + - - +
257C ALA* 3.0 29.6 + - - +
268C TRP* 4.4 1.1 - - - -
597C ASP* 3.9 25.3 + - + +
607C ILE 5.0 0.6 + - - -
608C PHE* 4.0 18.8 + - + +
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Residues in contact with GLY 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C SER* 3.9 0.2 - - - -
253C ALA* 1.3 79.5 - - - +
255C ASP* 1.3 56.6 + - - +
257C ALA* 3.9 0.9 - - - +
258C LYS* 3.0 30.8 + - - +
263C GLU* 5.2 1.7 - - - +
268C TRP* 4.0 16.7 + - - -
608C PHE* 2.9 24.2 + - - +
609C PHE* 4.4 15.0 - - - -
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Residues in contact with ASP 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ALA* 3.0 26.9 - - - +
251C GLY* 3.9 2.3 - - - -
252C SER* 3.1 32.4 + - - +
254C GLY* 1.3 75.7 - - - +
256C PHE* 1.3 64.3 + - - +
258C LYS* 3.5 6.0 + - - +
259C ALA* 3.1 24.6 + - - +
610C ALA 4.3 6.1 - - - +
612C PRO* 5.5 6.9 - - - +
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Residues in contact with PHE 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C PHE* 3.8 21.8 - + + -
236C ILE* 4.2 28.7 - - + -
237C ALA 5.6 0.4 - - - -
238C ARG* 4.2 26.5 - - - -
246C ASN* 4.3 9.4 - - + -
247C PHE* 3.4 54.7 - + + +
250C ALA* 4.0 23.5 - - + +
252C SER 3.2 8.7 + - - +
253C ALA* 3.6 8.7 - - - +
255C ASP* 1.3 80.6 - - - +
257C ALA* 1.3 66.0 + - - +
259C ALA* 3.4 5.2 + - - +
260C ALA* 3.1 20.5 + - + +
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C PHE* 3.8 11.7 - - + -
253C ALA 3.0 9.9 + - - +
254C GLY 3.9 1.6 - - - +
255C ASP 3.3 0.2 - - - -
256C PHE* 1.3 79.0 - - - +
258C LYS* 1.3 59.6 + - - +
260C ALA 3.1 1.6 + - - -
261C GLY 3.1 4.7 + - - -
262C LEU* 3.0 44.3 + - + +
263C GLU 5.2 0.2 - - - -
268C TRP* 3.4 44.9 - - + +
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Residues in contact with LYS 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 5.2 0.5 - - - +
254C GLY 3.0 19.0 + - - +
255C ASP* 3.8 6.7 - - - +
257C ALA* 1.3 77.0 - - - +
259C ALA* 1.3 61.4 + - - +
261C GLY* 3.2 13.7 + - - +
262C LEU 4.9 0.2 - - - +
263C GLU* 3.0 47.5 + - + +
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Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.0 22.0 - - - +
250C ALA* 6.0 2.5 - - + -
255C ASP 3.1 17.8 + - - +
256C PHE* 3.8 5.8 - - - +
258C LYS* 1.3 78.0 - - - +
260C ALA* 1.3 57.3 + - - +
261C GLY 3.3 0.2 - - - -
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.9 13.2 - - - -
38A ALA* 4.6 0.9 - - - +
39A ALA* 3.8 16.4 + - - -
236C ILE* 3.6 35.0 - - + +
256C PHE* 3.1 19.7 + - + +
257C ALA* 3.1 6.0 + - - +
259C ALA* 1.3 76.0 - - - +
261C GLY* 1.3 59.9 + - - +
262C LEU* 3.4 14.7 + - + +
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Residues in contact with GLY 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.4 5.8 - - - -
39A ALA* 4.4 8.5 - - - -
257C ALA 3.1 2.2 + - - -
258C LYS* 3.2 13.1 + - - -
259C ALA 3.3 1.4 + - - -
260C ALA* 1.3 78.3 - - - +
262C LEU* 1.3 60.3 + - - +
263C GLU* 3.2 8.2 + - - -
264C GLN* 2.7 39.1 + - - +
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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