Contacts of the helix formed by residues 339 - 344 (chain B) in PDB entry 2CKJ
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 339 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLN* 3.6 32.4 + - - -
145B GLY* 4.3 2.6 - - - -
337B PHE 3.0 12.5 + - - -
338B ALA* 1.3 77.2 - - - +
340B LYS* 1.3 60.4 + - - -
341B GLN* 3.0 14.2 + - - +
342B VAL* 3.2 17.3 + - - +
343B LYS* 3.7 10.5 + - - +
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Residues in contact with LYS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B SER* 3.8 11.0 + - - +
138B GLU 5.9 2.0 - - - -
141B ASN* 4.3 33.9 + - - +
142B ALA* 5.0 13.6 + - + +
144B GLN* 5.2 0.8 - - - +
145B GLY 4.7 0.8 - - - +
309B GLU* 4.5 9.1 + - - -
339B GLY* 1.3 71.0 - - - -
341B GLN* 1.3 68.2 + - - +
342B VAL 3.3 0.7 - - - -
343B LYS* 4.0 27.0 - - + +
344B SER* 2.9 32.6 + - - +
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Residues in contact with GLN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY* 4.3 0.6 - - - -
52B THR* 3.2 27.5 + - + +
69B SER* 4.0 27.3 - - - +
70B ALA* 3.8 13.8 - - - +
71B ASN* 3.5 29.3 + - - +
123B SER* 3.6 7.7 + - - -
142B ALA 4.4 3.3 - - - +
145B GLY* 3.3 31.5 + - - -
146B ASN* 3.1 25.8 + - - -
339B GLY 3.0 0.9 + - - +
340B LYS* 1.3 91.2 + - - +
342B VAL* 1.3 61.2 + - + +
343B LYS 3.5 0.2 - - - -
344B SER 4.1 0.9 - - - -
345B VAL* 3.7 21.0 + - - +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLY* 4.6 3.6 - - - +
71B ASN* 3.9 22.2 - - - +
74B LEU* 6.2 1.1 - - + -
262B THR* 4.9 11.5 - - + +
337B PHE* 5.0 5.2 - - + -
338B ALA* 4.4 13.2 - - + +
339B GLY 3.2 10.5 + - - +
341B GLN* 1.3 78.6 - - + +
343B LYS* 1.3 64.6 + - - +
344B SER 3.3 1.3 - - - -
345B VAL* 3.8 5.3 - - - +
346B ALA* 2.9 31.3 + - + +
3006B FAD 4.0 51.1 - - + -
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLN* 4.4 8.2 + - - -
304B PRO* 3.8 0.7 - - - +
305B LEU* 3.4 28.0 + - + +
306B SER* 2.9 34.0 + - - +
309B GLU* 3.3 27.5 + - - +
334B LEU* 2.9 27.9 + - + +
335B ARG* 4.4 2.0 - - - +
337B PHE* 2.9 42.1 + - + +
338B ALA* 4.8 0.7 - - + -
339B GLY* 3.7 23.7 + - - +
340B LYS* 3.7 22.3 + - + +
341B GLN 3.5 0.2 - - - -
342B VAL* 1.3 81.5 - - - +
344B SER* 1.4 57.7 + - - +
345B VAL 3.6 0.5 + - - -
346B ALA 3.8 1.0 - - - +
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Residues in contact with SER 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 4.1 27.0 - - - +
69B SER* 3.9 20.7 + - - -
304B PRO* 3.6 17.5 - - - +
306B SER* 3.8 19.0 + - - -
340B LYS* 2.9 24.1 + - - +
341B GLN 4.6 0.4 - - - -
342B VAL 3.3 0.8 - - - +
343B LYS* 1.4 79.4 - - - +
345B VAL* 1.4 65.2 + - - +
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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