Contacts of the helix formed by residues 329 - 334 (chain A) in PDB entry 1MUC
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 PHE 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A VAL* 3.9 6.5 - - + -
139A ALA 3.2 25.6 - - - +
140A TRP* 3.7 30.5 - + + -
141A THR* 3.3 37.0 - - - -
167A LYS* 5.5 0.4 - - + -
301A THR* 4.9 2.0 - - + -
303A LEU* 3.7 29.8 - - + -
327A GLU* 2.8 41.2 + - + -
328A LEU* 1.3 72.5 - - - +
330A GLY* 1.3 66.8 + - - +
331A PRO* 3.4 3.8 - - - -
332A LEU* 2.9 26.2 + - + +
333A LEU* 3.8 18.6 + - + -
345A TYR* 3.9 3.8 - - - -
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Residues in contact with GLY 330 (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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301A THR* 4.9 3.7 + - - +
303A LEU* 4.4 16.9 - - - +
304A GLU 3.3 19.1 - - - -
305A GLY* 4.9 0.2 - - - -
309A THR* 4.5 1.5 + - - -
327A GLU 4.6 1.2 + - - -
328A LEU* 3.5 1.6 - - - +
329A PHE* 1.3 82.9 - - - +
331A PRO* 1.3 69.7 - - - +
333A LEU* 3.0 23.5 + - - +
334A LEU* 4.0 8.0 - - - +
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Residues in contact with PRO 331 (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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304A GLU 3.6 1.1 - - - +
306A SER* 3.6 31.0 - - - +
309A THR* 3.2 21.8 - - + +
329A PHE 3.6 0.2 - - - -
330A GLY* 1.3 87.6 - - - +
332A LEU* 1.3 60.9 + - - +
333A LEU 3.1 1.5 + - - -
334A LEU* 3.3 27.6 + - + +
337A GLU* 3.7 21.8 - - - +
343A PRO* 3.8 15.7 - - + -
345A TYR* 3.3 23.1 - - + +
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Residues in contact with LEU 332 (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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19A ILE* 3.9 17.2 - - - +
140A TRP* 3.9 11.4 - - + -
162A ARG* 3.8 36.1 - - - +
163A HIS* 3.8 20.4 - - + +
329A PHE* 2.9 19.4 + - + +
331A PRO* 1.3 76.2 - - - +
333A LEU* 1.3 60.8 + - - +
334A LEU 3.4 3.1 + - - +
345A TYR* 3.6 46.9 - - + -
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Residues in contact with LEU 333 (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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18A THR* 3.0 16.3 - - + -
19A ILE* 2.9 44.1 + - + -
20A ARG* 5.9 0.7 - - - +
140A TRP* 3.7 28.3 - - + -
303A LEU* 3.8 28.7 - - + -
329A PHE* 3.8 28.7 - - + -
330A GLY* 3.0 13.2 + - - +
332A LEU* 1.3 76.6 - - - +
334A LEU* 1.3 62.4 + - + +
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Residues in contact with LEU 334 (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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16A LEU* 3.8 32.1 - - + -
17A PRO 3.7 2.0 - - - +
18A THR* 3.9 22.2 - - + -
19A ILE* 4.7 3.4 - - - +
32A GLN* 3.9 20.0 - - + -
34A LEU* 5.1 2.5 - - + -
303A LEU 5.8 1.6 - - - +
304A GLU 5.1 0.2 - - - +
305A GLY* 3.7 30.3 - - - -
330A GLY 4.0 8.7 - - - +
331A PRO* 3.3 15.6 + - + +
332A LEU 4.5 3.3 - - - +
333A LEU* 1.3 81.4 - - + +
335A THR* 1.3 62.5 + - - +
336A GLU 3.5 11.6 - - - +
337A GLU* 4.0 17.2 - - + +
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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