Contacts of the helix formed by residues 343 - 352 (chain E) in PDB entry 4K81
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 GLY 343 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228E PHE 5.1 0.2 - - - -
229E LEU* 3.7 20.2 - - - +
230E SER 5.4 3.4 - - - -
339E LEU* 2.8 27.8 + - - +
340E LEU 4.0 3.1 + - - -
341E LYS 3.7 1.4 - - - -
342E TYR* 1.3 71.8 - - - +
344E MET* 1.3 66.9 + - - -
345E GLN 2.9 1.9 + - - -
346E LEU* 3.1 18.7 + - - +
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Residues in contact with MET 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E GLN* 6.1 1.3 - - - -
229E LEU* 3.8 45.2 + - + +
342E TYR 3.8 0.4 + - - -
343E GLY* 1.3 70.3 - - - -
345E GLN* 1.3 62.9 + - - +
347E TYR* 2.9 31.2 + - + +
348E GLN* 2.9 45.7 + - + +
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Residues in contact with GLN 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E HIS* 3.5 44.2 - - + +
342E TYR* 3.6 14.5 + - + +
343E GLY 2.9 1.2 + - - -
344E MET* 1.3 78.9 - - - +
346E LEU* 1.3 52.5 + - - +
348E GLN* 3.4 12.0 + - - +
349E ASN* 2.7 62.9 + - - -
355E GLN* 5.0 5.7 + - - -
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Residues in contact with LEU 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E GLU* 3.1 36.1 - - + +
167E HIS* 5.4 0.7 - - + -
194E TYR* 4.1 9.3 - - + -
197E PHE* 3.5 21.5 - - + -
338E ARG* 3.8 46.7 - - + +
339E LEU* 4.0 19.1 - - + +
342E TYR* 3.6 18.2 - - + -
343E GLY 3.1 9.9 + - - +
345E GLN* 1.3 74.9 - - - +
347E TYR* 1.3 65.1 + - - +
349E ASN* 3.2 14.9 + - - +
350E TYR* 3.1 19.1 + - - +
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Residues in contact with TYR 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E PHE* 3.6 32.2 - + + -
225E LEU* 4.2 32.0 - - + +
229E LEU* 3.5 32.1 - - + -
343E GLY 4.2 0.2 + - - -
344E MET* 2.9 15.4 + - + +
346E LEU* 1.3 75.3 - - - +
348E GLN* 1.3 78.1 + - - +
350E TYR* 3.3 7.5 + + - +
351E MET* 2.8 71.1 + - + +
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Residues in contact with GLN 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E MET* 2.9 48.8 + - + +
345E GLN* 3.8 16.8 - - - +
347E TYR* 1.3 90.0 - - - +
349E ASN* 1.3 64.7 + - - +
351E MET* 4.6 1.9 - - - +
352E HIS* 2.9 63.5 + - - +
355E GLN* 5.5 3.2 + - - +
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Residues in contact with ASN 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E ARG* 3.0 27.7 + - - +
166E ASP* 3.2 36.5 + - + +
167E HIS* 3.1 31.0 + - - +
194E TYR* 3.5 6.4 + - + +
345E GLN* 2.7 49.6 + - - +
346E LEU* 3.2 17.9 + - - +
348E GLN* 1.3 72.9 - - - +
350E TYR* 1.3 64.4 + - - +
352E HIS 3.4 8.0 + - - -
353E PRO* 3.7 2.8 - - - +
355E GLN* 5.0 3.0 - - - +
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Residues in contact with TYR 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR* 4.1 31.8 + + + +
194E TYR* 3.5 41.7 + + + -
197E PHE* 3.7 44.6 + + + -
198E LYS* 4.1 25.3 - - + +
346E LEU 3.1 10.5 + - - +
347E TYR* 3.7 9.2 - + - +
349E ASN* 1.3 79.9 - - - +
351E MET* 1.3 84.6 + - + +
352E HIS 3.5 0.5 + - - -
353E PRO* 3.7 13.4 - - - +
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Residues in contact with MET 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.9 23.3 - - + -
32B TYR* 3.8 29.2 - - + +
34B PRO* 3.2 19.9 - - - +
61B GLN* 5.9 0.2 - - - -
347E TYR* 2.8 61.0 + - + +
348E GLN* 3.2 2.2 + - - +
350E TYR* 1.3 99.4 - - + +
352E HIS* 1.3 83.4 + - + +
353E PRO* 3.6 2.7 - - - -
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Residues in contact with HIS 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PRO* 4.4 6.7 - - + -
61B GLN* 3.5 24.3 + - - -
63B GLU* 5.6 1.6 + - - -
131E ARG* 3.1 14.6 + - - -
348E GLN* 2.9 46.1 + - + +
349E ASN 3.5 2.2 - - - +
351E MET* 1.3 96.5 + - + +
353E PRO* 1.3 67.3 - - - +
354E TYR 3.0 4.3 + - - -
355E GLN* 3.5 28.6 + - + +
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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