Contacts of the helix formed by residues 335 - 350 (chain A) in PDB entry 2KXL
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 PRO 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A CYS 4.6 0.2 - - - +
332A SER 5.0 1.3 - - - +
333A SER 3.8 7.0 - - - +
334A SER* 1.4 86.5 - - - +
336A GLU* 1.3 64.0 + - + +
337A ILE 3.2 0.7 - - - -
338A ALA* 3.2 8.1 + - + +
339A GLU* 2.9 38.1 + - + +
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Residues in contact with GLU 336 (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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334A SER* 3.3 7.4 - - - +
335A PRO* 1.3 85.0 - - + +
337A ILE* 1.3 59.2 + - + +
339A GLU* 3.8 7.2 - - + +
340A ILE* 2.9 55.1 + - + +
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Residues in contact with ILE 337 (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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238A LYS 5.2 2.9 - - - +
239A LEU* 3.3 41.7 - - + -
240A GLY 5.1 1.6 - - - +
243A VAL* 3.4 34.5 - - + -
327A PHE* 4.6 9.4 - - + -
330A LEU* 4.0 6.1 - - + +
331A CYS* 3.8 22.2 - - + +
334A SER* 3.4 27.2 + - - +
335A PRO 3.2 0.4 - - - -
336A GLU* 1.3 77.3 - - + +
338A ALA* 1.3 54.8 + - - +
340A ILE* 4.2 4.7 - - + +
341A PHE* 2.6 41.6 + - + +
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Residues in contact with ALA 338 (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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331A CYS* 3.4 36.5 - - - +
334A SER 3.3 2.9 + - - +
335A PRO* 3.2 11.6 + - + +
337A ILE* 1.3 79.8 - - - +
339A GLU* 1.3 64.1 - - - +
341A PHE* 3.8 2.1 - - - +
342A ARG* 2.9 31.2 + - - +
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Residues in contact with GLU 339 (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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335A PRO* 2.9 24.8 + - + +
336A GLU* 3.8 10.3 - - - +
337A ILE 3.3 0.2 - - - -
338A ALA* 1.3 83.6 - - - +
340A ILE* 1.3 60.5 + - + +
342A ARG* 3.5 20.3 + - - +
343A LYS* 2.9 53.7 + - - +
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Residues in contact with ILE 340 (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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238A LYS* 3.3 53.6 - - + +
239A LEU* 6.6 0.4 - - + -
336A GLU* 2.9 45.7 + - + +
337A ILE* 4.2 5.4 - - + +
339A GLU* 1.3 76.5 - - + +
341A PHE* 1.3 60.5 + - - +
343A LYS* 3.3 10.6 + - + +
344A THR* 3.0 29.3 + - - -
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Residues in contact with PHE 341 (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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235A LEU* 4.0 20.2 - - + +
301A LEU 3.0 27.8 - - - -
302A ILE* 4.1 9.4 - - - -
327A PHE* 3.0 36.3 - + + -
328A GLN* 6.1 2.7 - - + -
331A CYS* 3.6 20.0 - - - -
337A ILE* 2.6 28.4 + - + +
338A ALA 3.8 2.5 - - - +
340A ILE* 1.3 75.9 - - - +
342A ARG* 1.3 58.4 + - + +
344A THR* 3.0 12.0 - - + +
345A ALA* 2.8 35.7 + - + +
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Residues in contact with ARG 342 (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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338A ALA 2.9 20.8 + - - +
339A GLU* 3.9 21.5 + - - +
341A PHE* 1.3 75.6 - - + +
343A LYS* 1.3 61.3 + - + +
345A ALA* 4.0 6.3 - - + -
346A LEU* 2.7 60.2 + - + +
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Residues in contact with LYS 343 (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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339A GLU* 2.9 50.9 + - + +
340A ILE* 3.7 12.3 - - + +
341A PHE 3.3 0.2 - - - -
342A ARG* 1.3 80.4 - - + +
344A THR* 1.3 57.7 + - - +
346A LEU* 3.4 8.4 + - + +
347A GLU* 2.9 36.0 + - + +
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Residues in contact with THR 344 (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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235A LEU* 3.7 34.4 - - + +
238A LYS* 2.7 31.3 + - + +
340A ILE 3.0 14.0 + - - +
341A PHE* 3.0 20.9 - - + +
343A LYS* 1.3 74.8 - - - +
345A ALA* 1.3 62.2 + - - +
347A GLU* 3.7 6.2 - - - +
348A ARG* 2.7 40.7 + - - +
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Residues in contact with ALA 345 (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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302A ILE* 4.6 22.7 - - + +
341A PHE* 2.8 35.8 + - + +
342A ARG* 3.7 9.0 - - + +
344A THR* 1.3 78.6 - - - +
346A LEU* 1.3 56.2 + - + +
348A ARG* 3.9 5.0 - - - +
349A ARG* 2.8 36.6 + - - +
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Residues in contact with LEU 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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342A ARG* 2.7 49.2 + - + +
343A LYS* 3.8 7.6 - - + +
345A ALA* 1.3 74.9 - - + +
347A GLU* 1.3 59.8 + - + +
349A ARG* 4.0 8.8 - - + +
350A GLY* 2.8 26.2 + - - -
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Residues in contact with GLU 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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343A LYS* 2.9 21.2 + - + +
344A THR* 3.8 7.2 - - - +
346A LEU* 1.3 76.0 - - + +
348A ARG* 1.3 63.7 + - + +
350A GLY* 3.5 7.6 + - - -
351A ALA* 3.9 9.2 + - - +
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Residues in contact with ARG 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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234A PRO* 4.7 14.8 - - - +
235A LEU* 4.4 16.9 - - - +
298A GLU* 3.1 33.3 + - - +
299A MET* 4.8 11.7 - - + +
302A ILE* 3.9 25.9 - - + +
344A THR* 2.7 30.6 + - - +
345A ALA* 3.9 5.6 - - - +
347A GLU* 1.3 73.3 - - + +
349A ARG* 1.3 61.1 + - - +
351A ALA 3.1 24.6 - - - +
352A ALA* 3.9 4.9 + - - -
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Residues in contact with ARG 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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302A ILE* 5.8 5.6 - - + +
303A SER* 5.8 5.0 + - - +
345A ALA 2.8 20.2 + - - +
346A LEU* 4.0 11.4 - - + +
348A ARG* 1.3 73.1 - - - +
350A GLY* 1.3 70.0 + - - +
351A ALA* 3.0 5.5 + - - -
352A ALA 4.5 1.4 + - - -
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Residues in contact with GLY 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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346A LEU 2.8 19.5 + - - -
347A GLU* 3.5 4.5 + - - -
348A ARG 3.3 1.0 - - - -
349A ARG* 1.3 79.9 - - - +
351A ALA* 1.3 63.0 + - - +
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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