Contacts of the helix formed by residues 141 - 146 (chain L) in PDB entry 5M32
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 ALA 141 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11L THR* 2.5 32.0 + - + +
137L ALA* 4.8 0.3 - - - +
140L SER* 1.3 70.0 - - - +
142L SER* 1.3 63.7 + - - +
143L ALA 3.4 2.5 - - - +
144L MET* 3.7 27.8 - - + -
145L LEU* 3.4 23.7 + - + +
182L ALA* 4.4 12.6 - - + -
186L ASP* 3.4 17.9 - - + +
188L TYR 5.7 0.2 - - - +
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Residues in contact with SER 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K TYR* 3.5 17.8 + - - -
107L TYR* 5.7 1.6 - - - -
136L LYS* 5.3 2.5 - - - -
137L ALA 4.3 12.2 - - - +
138L GLY* 3.1 7.2 - - - -
139L GLY* 2.4 42.0 + - - +
140L SER 3.2 4.6 + - - -
141L ALA* 1.3 78.2 - - - +
143L ALA* 1.3 57.8 + - - +
144L MET 3.2 2.5 + - - -
145L LEU* 5.0 0.2 - - - +
146L GLN* 3.2 26.9 + - - +
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Residues in contact with ALA 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K TYR* 4.0 23.8 - - + -
140L SER 5.1 0.4 + - - -
141L ALA 3.4 0.6 - - - -
142L SER* 1.3 76.9 - - - +
144L MET* 1.3 59.5 + - - +
146L GLN* 4.8 0.4 - - - -
147L PRO* 4.3 4.7 - - - -
143W GLU* 3.3 27.1 - - + +
144W GLN* 3.2 46.4 + - - +
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Residues in contact with MET 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L SER 5.3 0.9 - - - +
141L ALA* 3.7 28.3 - - + -
142L SER 3.2 0.6 - - - -
143L ALA* 1.3 78.9 - - - +
145L LEU* 1.3 68.8 + - + +
146L GLN 3.3 0.9 - - - -
147L PRO* 3.6 9.5 - - - +
148L LEU* 4.6 2.6 + - - +
182L ALA* 4.0 12.1 - - + -
185L ARG* 3.6 25.4 - - + -
186L ASP* 3.4 42.4 - - + +
25V VAL* 5.0 4.5 - - + -
143W GLU* 3.6 36.1 - - + +
147W GLY* 3.7 27.9 - - - -
148W MET 3.8 1.0 + - - -
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Residues in contact with LEU 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L THR* 3.7 20.9 - - + -
13L LEU* 4.6 2.5 - - + -
137L ALA* 4.0 19.1 - - + -
141L ALA* 3.4 14.8 + - + +
144L MET* 1.3 77.8 - - + +
146L GLN* 1.3 65.2 + - - +
147L PRO 3.5 0.2 - - - -
148L LEU* 3.4 12.7 + - - +
149L LEU* 3.3 28.6 + - + +
178L VAL* 3.3 41.0 - - + +
179L PHE* 3.7 34.8 - - + -
181L SER* 6.0 0.4 - - - -
182L ALA* 3.8 13.0 - - + +
147W GLY 6.2 0.7 - - - +
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Residues in contact with GLN 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K TYR* 3.3 17.5 - - + +
27K ALA 5.2 0.2 + - - -
135L PHE* 3.3 35.3 - - - -
136L LYS* 3.2 38.8 + - - +
137L ALA* 4.0 5.1 + - - +
142L SER 3.2 19.7 + - - +
145L LEU* 1.3 79.4 - - - +
147L PRO* 1.3 62.5 - - + +
148L LEU 3.3 0.2 + - - -
149L LEU* 3.6 4.1 - - - +
150L ASP* 2.9 28.8 + - - +
176W ARG* 3.3 37.5 - - + +
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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