Contacts of the helix formed by residues 345 - 350 (chain A) in PDB entry 4E1O
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 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PHE 4.1 10.5 - - - +
105A THR* 3.4 12.9 - - + +
106A TRP* 2.9 23.0 + - - +
325A GLN* 4.0 3.7 + - - +
337A HIS* 2.9 27.4 + - - -
340A SER* 4.1 17.3 + - - +
343A ALA 3.6 5.8 + - - +
344A THR* 1.3 73.2 - - - +
346A PHE* 1.3 64.8 + - - +
347A MET* 3.2 4.5 + - + +
348A HIS* 3.2 36.1 + - + +
349A TRP* 3.5 11.7 + - - +
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Residues in contact with PHE 346 (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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103A GLY 4.5 3.0 + - - +
104A PHE 3.6 4.8 + - - -
105A THR* 4.9 0.2 - - - +
113A THR* 3.8 44.1 + - + -
116A GLU* 4.0 15.3 - - + -
117A MET* 3.8 19.1 - - + -
135A HIS* 4.0 3.1 - + - -
144A GLY 3.8 14.6 - - - -
145A VAL* 3.5 27.8 - - + +
344A THR* 3.7 14.8 + - + -
345A ASP* 1.3 67.2 - - - +
347A MET* 1.3 64.1 + - - +
348A HIS 3.0 2.7 - - - -
349A TRP* 2.9 41.9 + + - +
350A GLN* 3.4 12.9 - - - +
355A ARG* 3.6 38.1 - - - +
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Residues in contact with MET 347 (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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104A PHE* 3.0 27.5 + - + +
105A THR* 3.8 21.1 - - + -
330A VAL* 4.4 10.1 - - + +
331A ASN* 6.1 0.2 - - - -
332A PRO* 5.7 0.4 - - + -
335A LEU* 3.8 24.5 - - + +
345A ASP* 4.4 3.6 - - + +
346A PHE* 1.3 75.8 - - - +
348A HIS* 1.3 92.9 + - + +
349A TRP 3.2 0.4 - - - -
350A GLN* 3.3 20.0 - - - +
352A PRO 4.5 2.9 - - - +
353A LEU* 3.5 35.7 - - + +
199B LYS* 2.7 31.8 + - - +
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Residues in contact with HIS 348 (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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324A LEU 3.7 0.9 - - - +
325A GLN* 3.4 53.6 - - + +
328A PHE* 3.4 23.4 + - - +
329A SER* 3.8 25.8 + - - -
330A VAL* 3.4 29.3 + - + +
345A ASP* 3.2 28.1 + - + +
346A PHE 3.0 1.2 - - - -
347A MET* 1.3 103.1 + - + +
349A TRP* 1.3 59.3 + - - +
350A GLN 3.5 0.7 - - - -
199B LYS* 5.7 0.4 + - - -
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Residues in contact with TRP 349 (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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135A HIS* 3.5 22.9 - + - -
143A GLY* 3.6 30.1 - - - -
144A GLY 4.4 0.4 - - - -
145A VAL* 3.8 23.8 - - + -
147A GLN* 3.0 19.4 + - - -
156A ILE* 4.1 4.7 - - - +
318A VAL* 4.2 8.1 - - + -
321A LYS* 3.6 35.4 - - + -
324A LEU* 3.7 32.7 - - + +
325A GLN* 3.4 24.2 - - + +
328A PHE* 4.1 6.9 - - - -
344A THR* 4.0 19.2 - - + +
345A ASP 3.5 18.9 + - - -
346A PHE* 2.9 28.8 + + + +
348A HIS* 1.3 81.1 - - - +
350A GLN* 1.3 58.8 + - - +
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Residues in contact with GLN 350 (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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145A VAL* 5.4 0.6 - - + +
146A LEU 5.0 0.5 - - - +
147A GLN* 3.9 17.8 - - - +
156A ILE* 4.1 6.1 - - - -
328A PHE* 3.6 16.7 - - - -
346A PHE 3.4 12.7 - - - +
347A MET* 3.3 7.2 - - - +
348A HIS 3.5 0.8 - - - -
349A TRP* 1.3 80.3 - - + +
351A ILE* 1.3 59.9 + - - +
352A PRO* 3.0 26.5 + - + +
353A LEU 2.9 27.9 + - - -
354A SER 3.6 10.9 + - - -
355A ARG* 2.8 40.1 + - - +
358A ARG* 5.1 3.1 + - - -
199B LYS* 2.9 25.6 + - - -
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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