Contacts of the helix formed by residues 167 - 172 (chain A) in PDB entry 3PMM
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 ASP 167 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ASN* 4.0 12.0 - - - +
153A HIS* 2.7 35.3 - - - -
165A TRP* 3.6 16.2 - - - +
166A ASP* 1.3 74.5 + - - +
168A THR* 1.3 66.0 + - - +
169A LEU 3.2 0.4 - - - -
170A MSE 3.2 4.5 + - - +
171A MSE 3.0 36.4 + - + +
213A HIS* 4.9 4.2 + - - -
234A TRP* 3.6 33.7 - - + +
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 3.7 22.3 - - + +
143A MSE 4.7 1.1 - - + -
151A MSE 4.1 25.3 + - + +
152A GLN 5.7 0.2 - - - +
153A HIS* 3.2 27.7 + - - +
165A TRP 3.5 7.6 + - - -
166A ASP 3.3 1.4 - - - -
167A ASP* 1.3 79.5 - - - +
169A LEU* 1.3 64.6 + - - +
172A THR* 3.0 21.5 + - - -
173A VAL* 3.2 12.3 + - + -
199A HIS* 3.6 29.6 - - + +
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Residues in contact with LEU 169 (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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166A ASP 4.0 6.2 + - - +
167A ASP 3.2 0.6 - - - -
168A THR* 1.3 76.1 - - - +
170A MSE 1.3 60.8 + - - +
173A VAL* 3.3 20.6 + - + +
174A LEU 2.9 28.4 + - - -
195A GLN 3.9 6.7 - - - +
196A PHE* 3.9 41.7 - - + +
199A HIS* 3.6 44.6 - - + +
211A TRP* 4.7 4.9 - - + -
235A LEU* 3.5 25.6 - - + -
238A VAL* 3.7 18.9 - - + +
239A ILE* 5.7 0.2 - - + -
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Residues in contact with MSE 170 (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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69A VAL* 5.1 4.3 - - + -
72A TYR* 3.6 32.3 - - + -
166A ASP 4.9 0.8 + - - -
167A ASP 3.2 8.0 + - - +
169A LEU* 1.3 80.5 - - - +
171A MSE 1.3 84.9 + - + +
174A LEU* 4.0 11.5 - - + +
175A PRO* 3.4 10.0 - - - +
234A TRP* 4.3 21.8 - - + +
237A MSE 3.7 26.2 - - + -
238A VAL* 3.7 31.3 - - + +
241A ASP* 5.1 0.9 - - - +
369A LEU* 5.4 0.9 - - + -
388A FMT 2.8 43.2 - - - +
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Residues in contact with MSE 171 (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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65A TRP* 3.7 34.8 - - + -
69A VAL* 3.8 19.5 - - + -
107A VAL* 3.2 22.0 - - + +
108A ASN* 4.3 9.2 - - - +
110A MSE 3.6 0.9 - - - +
111A ALA* 3.3 38.0 + - + -
167A ASP* 3.0 31.5 + - + +
168A THR 4.5 0.4 - - - +
170A MSE 1.3 88.0 - - + +
172A THR* 1.3 60.7 + - - +
175A PRO* 3.4 5.3 - - - +
234A TRP* 3.7 41.7 - - + -
388A FMT 4.1 2.7 - - - -
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Residues in contact with THR 172 (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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106A ASN 4.7 0.2 - - - -
107A VAL* 2.8 41.7 + - - -
110A MSE 3.4 19.6 - - + +
138A TRP* 4.7 1.3 - - + -
139A ALA* 4.2 14.4 - - + -
143A MSE 4.1 13.4 - - + +
151A MSE 3.9 22.9 - - + -
168A THR* 3.0 10.8 + - - -
171A MSE 1.3 77.8 - - - +
173A VAL* 1.3 61.2 + - - +
175A PRO* 3.4 7.0 - - - +
176A LEU* 3.0 25.2 + - + +
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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