Contacts of the helix formed by residues 338 - 347 (chain B) in PDB entry 2JDQ
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 338 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299B ARG* 5.4 1.2 + - - -
302B VAL* 4.2 1.6 - - - +
335B LEU 3.2 9.3 + - - -
336B ASN 3.2 7.7 + - - -
337B CYS* 1.3 83.1 - - - +
339B ALA* 1.3 63.6 + - - +
340B LEU* 3.3 3.5 + - - +
341B GLN* 4.0 20.3 + - - +
342B SER* 4.2 9.9 + - - -
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Residues in contact with ALA 339 (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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302B VAL* 3.6 21.1 - - + -
305B LEU* 4.6 3.8 - - + +
320B VAL* 5.0 0.7 - - + -
334B ILE* 3.6 37.9 + - + +
335B LEU* 4.3 6.7 + - + +
337B CYS 3.4 1.6 - - - -
338B SER* 1.3 76.1 - - - +
340B LEU* 1.3 59.4 + - - +
342B SER* 3.1 7.0 + - - -
343B LEU* 2.9 42.0 + - + +
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 4.0 15.0 + - + +
338B SER* 3.3 2.0 - - - +
339B ALA* 1.3 76.8 - - - +
341B GLN* 1.3 56.2 + - - +
343B LEU* 3.4 8.8 + - + +
344B LEU* 2.9 25.3 + - - +
362B ILE* 5.0 3.1 - - + -
365B ILE* 4.1 22.2 - - + -
375B THR* 3.1 56.5 - - + +
376B VAL* 3.7 17.9 - - + +
379B ALA* 3.9 14.8 - - + +
381B ILE* 3.5 26.7 - - + +
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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
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338B SER* 4.0 17.3 + - - +
339B ALA 3.3 0.6 - - - -
340B LEU* 1.3 77.4 - - - +
342B SER* 1.3 63.1 + - - +
344B LEU* 3.5 10.0 + - + +
345B HIS* 3.2 20.3 + - - +
379B ALA* 5.6 5.6 - - + -
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Residues in contact with SER 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B VAL* 4.4 5.9 + - - +
305B LEU* 4.0 20.6 - - - -
306B MET* 3.5 39.5 - - - +
338B SER 4.2 8.3 + - - -
339B ALA* 3.1 8.6 + - - -
341B GLN* 1.3 75.8 - - - +
343B LEU* 1.3 60.4 + - - +
345B HIS* 3.2 5.0 + - - +
346B LEU* 2.9 32.6 + - - +
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 4.4 11.0 - - + -
317B LEU* 3.5 32.5 - - + -
320B VAL* 5.2 1.6 - - + -
339B ALA* 2.9 34.5 + - + +
340B LEU* 3.7 9.0 - - + +
342B SER* 1.3 74.1 - - - +
344B LEU* 1.3 65.0 + - - +
346B LEU* 3.2 6.7 + - + +
347B LEU* 3.1 25.7 + - - +
358B ALA* 4.1 11.4 - - + +
361B THR* 3.7 28.7 - - + -
362B ILE* 4.3 21.5 - - + -
365B ILE* 4.3 14.6 - - + -
381B ILE* 4.9 0.7 - - + -
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Residues in contact with LEU 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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340B LEU 2.9 18.7 + - - +
341B GLN* 3.7 9.0 - - - +
342B SER 3.3 0.2 - - - -
343B LEU* 1.3 75.2 - - - +
345B HIS* 1.3 66.3 + - - +
347B LEU* 3.2 17.7 + - + +
348B SER* 3.9 6.1 + - - -
379B ALA 3.6 19.7 - - - +
380B ASN* 3.8 22.9 - - + +
381B ILE* 3.9 17.8 - - + +
384B ALA* 4.0 22.9 - - + -
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Residues in contact with HIS 345 (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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306B MET* 3.1 33.6 - - + +
341B GLN 3.2 10.1 + - - +
342B SER* 3.2 9.8 + - - +
343B LEU 3.2 0.2 - - - -
344B LEU* 1.3 79.1 - - - +
346B LEU* 1.3 71.4 + - + +
348B SER* 3.1 23.2 + - - -
349B SER* 4.0 2.1 + - - -
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Residues in contact with LEU 346 (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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305B LEU* 3.9 37.7 - - + +
306B MET* 4.5 0.7 - - + -
310B TYR* 6.0 2.7 - - + -
313B VAL* 4.0 22.0 - - + -
317B LEU* 4.0 24.9 - - + -
342B SER 2.9 20.5 + - - +
343B LEU* 3.2 7.1 + - + +
345B HIS* 1.3 88.0 - - + +
347B LEU* 1.3 60.7 + - - +
348B SER 3.1 0.7 - - - -
349B SER* 3.1 25.4 + - - +
354B ILE* 3.9 18.8 - - + -
355B LYS* 3.7 11.6 + - - -
358B ALA* 4.1 9.9 - - + -
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Residues in contact with LEU 347 (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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343B LEU 3.1 17.9 + - - +
344B LEU* 3.4 15.7 - - + +
345B HIS 3.2 1.0 - - - -
346B LEU* 1.3 75.2 - - - +
348B SER* 1.3 57.2 + - - +
349B SER 3.3 1.3 - - - -
355B LYS* 3.2 28.1 - - - +
358B ALA* 3.7 18.8 - - + -
359B CYS* 3.6 33.2 - - - +
362B ILE* 3.8 20.0 - - + -
381B ILE* 4.5 6.1 - - + +
384B ALA* 3.7 29.4 - - + -
385B LEU* 4.1 11.9 - - + -
388B ILE* 3.8 12.0 - - + +
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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