Contacts of the helix formed by residues 174 - 182 (chain D) in PDB entry 1M54
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 174 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D MET* 1.3 77.4 - - - +
175D SER* 1.3 64.1 + - - +
176D GLU* 4.0 4.4 + - - +
177D LYS* 3.0 42.5 + - - +
178D VAL* 3.3 15.5 - - - +
380D ASN 4.2 8.1 + - - -
383D THR* 5.6 3.4 - - - -
384D LYS* 4.4 29.4 - - - +
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Residues in contact with SER 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C ARG* 2.3 44.5 + - - -
174D SER* 1.3 67.0 - - - +
176D GLU* 1.3 69.7 + - - +
177D LYS 2.6 16.6 + - - -
178D VAL* 2.9 8.9 + - - -
179D ASP* 2.5 35.8 + - - +
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Residues in contact with GLU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C MET* 3.1 53.2 - - + +
383C THR* 3.6 19.8 - - - +
389C ARG* 4.4 1.2 + - - -
174D SER* 3.3 4.5 - - - +
175D SER* 1.3 103.4 + - - +
177D LYS* 1.3 58.7 + - - +
180D VAL* 2.7 21.7 - - - +
379D ARG* 4.5 6.7 - - - +
380D ASN* 4.2 18.8 - - - +
382D MET* 3.9 9.0 - - + +
383D THR* 3.0 42.3 + - - +
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Residues in contact with LYS 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D SER 4.3 11.2 - - - +
148D GLY* 5.2 7.2 - - - -
152D ILE* 5.2 6.5 - - + -
173D MET* 3.0 40.3 - - + +
174D SER* 3.0 24.1 + - - +
175D SER 2.6 5.5 + - - -
176D GLU* 1.3 74.8 - - - +
178D VAL* 1.4 54.7 + - - +
179D ASP 3.1 2.0 - - - -
180D VAL* 2.4 43.5 + - - +
181D LEU* 3.6 6.6 + - + +
304D GLU* 2.7 44.5 + - - -
380D ASN* 3.0 38.5 + - - +
381D TYR* 5.9 0.4 - - - -
384D LYS* 4.8 0.4 - - - +
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Residues in contact with VAL 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D MET* 4.2 23.6 - - + -
173D MET* 4.2 9.4 - - + -
174D SER 3.3 20.2 - - - +
175D SER* 2.9 8.5 + - - +
177D LYS* 1.4 71.3 - - + +
179D ASP* 1.3 61.4 + - - +
181D LEU* 3.6 5.4 + - - +
182D ARG* 2.8 48.3 + - + +
188D ILE* 3.8 29.5 - - + +
190D ARG* 5.2 6.3 - - - +
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Residues in contact with ASP 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C MET* 4.2 15.3 - - + -
386C LEU* 3.6 19.1 - - + +
387C SER* 2.9 34.2 + - - +
388C ASP 4.0 3.1 + - - -
389C ARG* 2.6 11.5 + - - -
175D SER* 2.5 42.3 + - - +
176D GLU* 4.5 0.3 - - - +
178D VAL* 1.3 78.7 - - - +
180D VAL* 1.3 62.5 + - - +
182D ARG* 4.0 18.0 - - - +
183D ALA* 3.6 17.8 + - - +
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Residues in contact with VAL 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C LEU* 5.4 7.6 - - + -
382C MET* 5.0 4.3 - - + -
386C LEU* 5.3 4.3 - - + -
152D ILE* 3.3 43.3 - - + -
176D GLU 2.7 23.6 - - - +
177D LYS* 2.4 38.2 + - - +
179D ASP* 1.3 68.8 - - - +
181D LEU* 1.3 62.4 + - + +
183D ALA* 2.9 25.8 + - - +
184D LEU* 3.2 14.7 + - + +
379D ARG* 4.5 19.3 - - - +
380D ASN* 4.9 2.5 - - - +
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Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D SER 5.3 7.2 - - - +
151D GLY* 3.4 36.1 - - - +
152D ILE* 3.5 15.7 - - + +
155D ALA* 3.9 9.6 - - + -
167D ILE* 4.3 17.3 - - + -
169D MET* 5.6 0.4 - - - -
177D LYS* 4.5 9.9 - - + +
178D VAL* 3.6 3.8 + - - +
180D VAL* 1.3 72.8 - - + +
182D ARG* 1.3 56.1 + - - +
183D ALA 2.9 4.9 - - - -
184D LEU* 2.7 27.3 + - + +
185D GLY 3.1 9.4 + - - -
186D ALA* 3.2 24.1 + - + +
188D ILE* 3.6 34.1 - - + -
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Residues in contact with ARG 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386C LEU 5.7 1.3 - - - +
388C ASP* 3.6 34.6 + - - +
178D VAL* 2.8 44.2 + - + +
179D ASP* 4.1 18.6 - - - +
180D VAL 3.2 0.2 - - - -
181D LEU* 1.3 76.9 - - - +
183D ALA* 1.3 59.2 + - - +
185D GLY* 3.7 8.5 + - - -
186D ALA 4.1 9.6 + - - +
188D ILE* 5.7 11.3 - - + +
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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