Contacts of the helix formed by residues 346 - 359 (chain A) in PDB entry 5KZX
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 GLU 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A GLY 4.9 0.9 - - - -
344A GLY 4.0 0.2 - - - +
345A PRO* 1.3 103.0 - - + +
347A PRO* 1.3 73.4 - - + +
348A LYS* 4.3 9.0 - - + +
349A SER* 2.9 30.9 + - - +
350A VAL* 3.0 20.6 + - - +
729A LEU 6.2 0.2 - - - +
732A PRO* 5.5 6.5 - - + -
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Residues in contact with PRO 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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299A LEU* 3.9 11.5 - - + +
301A LEU* 3.8 27.1 - - + -
305A GLY 3.5 17.3 - - - +
307A ALA* 3.9 5.2 - - + -
345A PRO 3.8 2.7 - - - +
346A GLU* 1.3 83.3 - - + +
348A LYS* 1.3 62.6 + - - +
350A VAL* 3.2 8.5 + - + +
351A VAL* 3.1 26.2 + - - +
728A PHE* 4.2 8.1 - - + +
729A LEU* 3.6 28.5 - - + +
732A PRO* 3.8 20.6 - - + -
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Residues in contact with LYS 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLU* 3.3 9.1 - - + +
347A PRO* 1.3 75.8 - - - +
349A SER* 1.3 57.3 + - - +
351A VAL* 3.4 5.5 + - - +
352A GLN* 3.0 27.3 + - - +
720A GLY 4.8 1.2 - - - +
721A GLU* 4.0 23.4 + - - +
722A THR* 5.3 0.7 - - - +
725A ARG* 3.6 18.4 - - - +
729A LEU* 3.4 42.1 + - + +
730A GLU* 2.6 40.3 + - - +
748A GLU* 4.4 6.9 - - - +
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Residues in contact with SER 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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344A GLY 3.9 4.3 - - - -
346A GLU* 2.9 36.2 + - - +
348A LYS* 1.3 74.0 - - - +
350A VAL* 1.3 66.5 + - - +
352A GLN* 3.2 11.6 + - - +
353A GLN* 2.8 47.0 + - - +
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Residues in contact with VAL 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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297A PHE* 4.2 7.9 - - + -
299A LEU* 3.9 16.2 - - + -
307A ALA* 3.3 39.9 - - + +
308A HIS* 3.8 4.0 - - - -
309A GLY* 3.5 29.6 - - - +
342A PHE* 4.2 5.4 - - + +
344A GLY* 3.5 15.7 - - - +
346A GLU 3.0 13.5 + - - +
347A PRO* 3.2 6.9 + - + +
349A SER* 1.3 75.8 - - - +
351A VAL* 1.3 64.1 + - - +
353A GLN* 3.3 9.1 + - - +
354A TYR* 3.0 22.7 + - - +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PHE* 5.2 4.0 - - + -
299A LEU* 4.1 15.9 - - + -
347A PRO 3.1 14.0 + - - +
348A LYS* 3.7 9.0 - - - +
349A SER 3.2 0.2 - - - -
350A VAL* 1.3 75.5 - - - +
352A GLN* 1.3 62.0 + - - +
354A TYR* 3.3 8.1 + - - +
355A LEU* 2.9 37.0 + - + +
635A ASN 4.4 0.4 - - - +
636A LEU* 3.6 46.9 - - + +
720A GLY 3.9 13.9 - - - +
722A THR* 4.2 17.9 - - + -
729A LEU* 4.6 3.8 - - + -
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Residues in contact with GLN 352 (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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177A ASN* 5.8 1.3 + - - +
348A LYS 3.0 17.8 + - - +
349A SER* 3.2 15.5 + - - +
351A VAL* 1.3 76.6 - - - +
353A GLN* 1.3 70.2 + - - +
355A LEU* 3.2 3.9 + - - +
356A ASP* 2.9 56.5 + - - +
360A TYR* 3.8 10.4 + - + +
719A ALA 3.2 26.5 - - - +
720A GLY* 3.7 13.9 - - - +
721A GLU* 5.4 3.6 - - - +
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Residues in contact with GLN 353 (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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177A ASN* 3.3 36.9 - - + +
178A ARG* 5.0 2.5 + - + -
342A PHE* 3.4 29.1 - - + +
343A LEU 3.3 10.0 + - - -
344A GLY* 2.9 45.3 + - - +
349A SER* 2.8 32.3 + - - +
350A VAL* 3.6 3.6 - - - +
352A GLN* 1.3 87.4 + - - +
354A TYR* 1.3 65.6 + - - +
356A ASP* 3.2 18.8 - - - +
357A VAL* 3.6 2.8 + - - +
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Residues in contact with TYR 354 (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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295A HIS* 4.7 1.0 + - - +
297A PHE* 3.5 57.8 - + + +
311A PHE* 3.7 18.8 - + + -
342A PHE* 3.7 22.0 - + + -
350A VAL 3.0 13.0 + - - +
351A VAL 3.5 6.7 - - - +
353A GLN* 1.3 76.0 - - - +
355A LEU* 1.3 68.0 + - + +
357A VAL* 3.0 18.2 + - - +
358A VAL* 3.1 39.7 + - + +
604A ALA* 3.2 30.8 - - - +
605A GLY 4.5 0.3 + - - -
636A LEU 4.3 6.7 - - - -
637A LEU* 4.1 25.7 + - + +
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Residues in contact with LEU 355 (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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351A VAL* 2.9 27.2 + - + +
352A GLN* 3.2 3.6 + - - +
354A TYR* 1.3 84.3 - - + +
356A ASP* 1.3 59.7 + - - +
358A VAL* 3.7 21.1 - - + -
359A GLY* 2.8 45.1 + - - +
360A TYR* 3.6 17.5 + - + -
361A PRO* 4.1 15.9 - - + -
635A ASN 5.2 0.7 - - - +
637A LEU 4.0 2.0 - - - +
638A GLY* 3.5 36.1 - - - +
720A GLY* 3.6 23.1 - - - +
721A GLU 5.0 2.0 - - - +
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Residues in contact with ASP 356 (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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178A ARG* 4.4 14.3 + - - +
198A PRO* 3.5 23.0 - - + +
352A GLN* 2.9 27.6 + - - +
353A GLN* 3.2 16.2 - - - +
355A LEU* 1.3 77.9 - - - +
357A VAL* 1.3 56.1 + - - +
359A GLY* 4.7 0.6 - - - -
360A TYR* 2.5 34.8 + - - -
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Residues in contact with VAL 357 (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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178A ARG* 3.5 36.8 - - - +
195A LEU* 3.9 20.0 - - + +
196A GLU 4.2 9.9 - - - +
198A PRO* 4.3 11.7 - - + +
311A PHE* 4.4 17.7 - - + -
340A TYR* 4.0 33.0 - - + +
342A PHE* 3.6 18.8 - - + -
353A GLN 3.9 1.1 - - - +
354A TYR 3.0 8.3 + - - +
356A ASP* 1.3 81.0 - - - +
358A VAL* 1.3 63.3 + - + +
359A GLY 3.5 0.4 + - - -
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 4.4 11.5 - - + +
311A PHE* 3.6 35.9 - - + -
354A TYR* 3.1 40.7 + - + +
355A LEU* 3.7 24.0 - - + -
357A VAL* 1.3 77.4 - - + +
359A GLY* 1.3 59.1 + - - +
604A ALA* 4.5 1.8 - - + +
605A GLY* 3.7 39.8 - - - +
608A ARG* 4.2 10.4 + - - -
609A TYR* 5.9 0.2 - - - -
637A LEU 5.2 0.9 - - - +
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Residues in contact with GLY 359 (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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355A LEU* 2.8 38.5 + - - +
356A ASP 4.7 1.1 - - - -
357A VAL 3.5 1.6 - - - -
358A VAL* 1.3 77.0 - - - +
360A TYR* 1.3 65.4 + - - -
361A PRO* 3.8 0.7 - - - +
605A GLY* 5.6 1.0 - - - +
608A ARG* 4.1 23.7 + - - +
638A GLY 5.2 1.4 - - - +
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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