Contacts of the helix formed by residues 336 - 341 (chain F) in PDB entry 6CP3
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 336 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161F VAL* 4.4 4.5 - - - -
315F ASP* 5.5 3.9 - - - -
334F VAL* 4.2 7.5 - - - -
335F LEU* 1.3 74.2 - - - +
337F ARG* 1.3 67.8 + - - +
338F GLY* 3.5 10.3 + - - -
339F ILE* 3.3 24.2 + - - +
340F SER* 3.3 15.1 + - - -
347F ALA* 3.5 13.4 + - - +
349F ASP* 4.8 7.0 - - - -
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Residues in contact with ARG 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B VAL* 4.2 33.4 + - - +
337B SER* 4.5 8.7 - - - -
342B THR* 4.6 6.7 - - - +
345B ILE* 5.4 4.5 - - - +
158F GLY 4.1 0.6 - - - -
159F ALA* 2.8 54.8 + - - +
160F GLY 5.3 0.8 + - - -
161F VAL* 3.7 13.3 - - + +
314F ALA* 5.9 0.4 - - - +
315F ASP* 2.4 41.6 + - - +
336F SER* 1.3 73.9 + - - +
338F GLY* 1.3 60.4 + - - +
340F SER* 2.7 26.9 + - - +
341F GLU* 3.0 33.4 + - + +
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Residues in contact with GLY 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F SER* 3.3 7.0 + - - -
337F ARG* 1.3 76.7 - - - +
339F ILE* 1.3 61.5 + - - +
341F GLU* 4.2 13.2 + - - +
342F LEU* 4.2 16.5 + - - +
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Residues in contact with ILE 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F SER* 3.3 17.5 + - - +
337F ARG 3.1 0.4 - - - -
338F GLY* 1.3 78.6 - - - +
340F SER* 1.3 65.0 + - - +
341F GLU 3.2 0.2 - - - -
342F LEU* 3.1 23.2 + - - +
343F GLY 3.9 2.6 + - - -
344F ILE* 4.0 24.5 + - + +
347F ALA* 3.8 25.8 - - + +
348F VAL 4.3 4.3 - - - +
349F ASP* 3.5 43.1 - - + +
350F PRO* 4.4 7.0 - - + -
411F GLN* 6.2 3.6 - - - +
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Residues in contact with SER 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F VAL* 3.4 18.0 - - - +
336F SER 3.3 4.9 + - - -
337F ARG* 2.7 29.4 + - - +
339F ILE* 1.3 78.2 - - - +
341F GLU* 1.3 62.5 + - - +
343F GLY* 3.3 9.5 + - - -
344F ILE 4.5 5.2 - - - -
345F TYR* 3.4 33.0 + - - -
347F ALA* 3.7 20.8 - - - +
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Residues in contact with GLU 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B VAL* 5.1 7.4 - - - +
370B GLY 4.9 3.5 - - - +
371B LEU* 3.4 41.3 - - + +
400B ARG* 3.5 26.0 + - - +
337F ARG* 3.0 36.4 + - + +
338F GLY* 4.5 9.3 - - - +
339F ILE 3.2 0.6 - - - -
340F SER* 1.3 78.7 + - - +
342F LEU* 1.3 65.9 + - + +
343F GLY* 3.1 1.5 + - - -
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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