Contacts of the helix formed by residues 357 - 370 (chain S) in PDB entry 5L4K
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 LEU 357 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326S GLN* 4.3 5.4 - - + +
329S HIS* 4.0 19.7 - - + -
330S LYS* 3.9 25.8 - - + -
333S ILE* 4.1 17.0 - - + -
347S GLN 3.0 30.3 - - - +
348S PHE* 4.1 20.9 - - + -
353S LEU* 3.3 30.5 - - + +
354S LYS* 3.8 6.6 + - - +
355S ARG 3.5 0.4 - - - -
356S SER* 1.3 77.6 - - - +
358S MET* 1.3 66.3 + - - +
359S PRO* 3.3 3.4 - - - -
360S TYR* 2.9 21.9 + - + +
361S PHE* 3.2 8.7 + - - +
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Residues in contact with MET 358 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354S LYS* 3.5 27.3 + - - +
355S ARG* 3.8 24.0 - - - +
356S SER 3.4 0.6 - - - -
357S LEU* 1.3 76.0 - - - +
359S PRO* 1.3 71.3 - - + +
361S PHE* 3.3 21.3 - - - +
362S LEU* 3.5 16.2 - - + +
382S PHE* 5.4 1.8 - - + -
31Y ASP* 3.5 37.7 - - + +
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Residues in contact with PRO 359 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355S ARG 4.9 1.6 - - - +
356S SER 3.9 11.7 - - - +
357S LEU 3.4 4.9 - - - -
358S MET* 1.3 91.0 - - + +
360S TYR* 1.3 69.4 + - + +
362S LEU* 2.9 18.3 + - + +
363S LEU 3.1 7.3 + - - -
378S VAL* 4.8 1.2 - - - +
382S PHE* 3.6 37.9 - - + -
385S LYS* 4.7 17.0 - - + +
386S PHE* 3.9 26.4 - - + -
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Residues in contact with TYR 360 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330S LYS* 3.4 61.9 + - + +
333S ILE* 4.3 16.6 - - + -
334S VAL* 3.9 22.9 - - + -
348S PHE* 4.3 10.3 - - + -
356S SER 4.3 4.5 - - - -
357S LEU* 2.9 27.6 + - + +
359S PRO* 1.3 77.7 - - + +
361S PHE* 1.3 57.0 + - - +
363S LEU* 2.6 33.9 + - + +
364S THR* 2.9 15.1 + - - -
386S PHE* 4.1 28.2 - + - -
389S ASP* 4.4 5.7 + - - -
391S THR* 4.2 17.0 + - + +
395S ILE* 4.8 3.6 - - + -
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Residues in contact with PHE 361 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345S ARG* 3.4 28.5 - - - -
348S PHE* 3.9 31.3 - + + -
357S LEU 3.2 3.6 + - - +
358S MET* 3.3 17.3 - - - +
359S PRO 3.1 0.6 - - - -
360S TYR* 1.3 78.1 - - - +
362S LEU* 1.3 68.0 + - + +
364S THR* 3.3 6.0 + - - -
365S GLN* 3.0 44.2 + - + +
33Y ASP* 5.5 8.1 - - - -
43Y TRP* 3.9 21.5 - + - -
46Y ASP* 3.9 26.2 - - + -
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Residues in contact with LEU 362 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358S MET* 3.5 22.4 - - + +
359S PRO* 2.9 6.9 + - + +
361S PHE* 1.3 82.5 - - + +
363S LEU* 1.3 65.7 + - - +
364S THR 3.3 0.4 - - - -
365S GLN* 3.8 18.3 - - + +
366S ALA* 3.6 11.3 + - - +
378S VAL* 3.3 33.6 - - + +
382S PHE* 3.9 30.1 - - + -
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Residues in contact with LEU 363 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334S VAL* 4.8 3.8 - - + -
337S LEU* 4.7 9.6 - - + -
359S PRO 3.1 5.7 + - - -
360S TYR* 2.6 31.7 + - + +
362S LEU* 1.3 71.1 - - - +
364S THR* 1.3 56.2 + - - +
366S ALA* 3.2 4.3 + - - +
367S VAL* 2.9 33.8 + - + +
375S PHE* 3.8 25.4 - - + -
378S VAL* 4.0 15.5 - - + -
379S LEU* 4.3 9.0 - - + -
386S PHE* 3.5 44.4 - - + -
395S ILE* 4.2 20.9 - - + -
398S LEU* 4.8 8.5 - - + -
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Residues in contact with THR 364 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333S ILE* 4.4 2.1 - - - +
337S LEU* 4.1 19.4 - - + +
342S ILE* 4.5 7.0 - - + -
343S PRO* 4.0 24.8 - - + +
348S PHE* 4.3 12.1 - - - -
360S TYR 2.9 12.9 + - - -
361S PHE 3.7 7.0 - - - -
363S LEU* 1.3 71.2 - - - +
365S GLN* 1.3 69.5 + - - +
366S ALA 3.0 1.6 - - - -
367S VAL* 4.2 5.2 - - - +
368S ARG* 2.9 29.3 + - + +
43Y TRP* 3.8 31.4 - - + -
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Residues in contact with GLN 365 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361S PHE* 3.0 34.9 + - + +
362S LEU* 3.8 22.7 - - + +
364S THR* 1.3 76.5 - - - +
366S ALA* 1.3 57.5 + - + +
368S ARG* 4.4 11.5 + - - +
369S THR* 3.1 24.6 + - - +
374S LYS* 5.5 2.0 - - - +
43Y TRP* 4.3 17.8 - - - -
46Y ASP* 3.3 39.7 + - - +
47Y ASN* 3.9 20.0 + - - +
49Y GLU* 5.5 0.3 - - - +
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Residues in contact with ALA 366 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362S LEU 3.6 9.1 + - - +
363S LEU 3.2 7.7 + - - +
364S THR 3.0 0.8 - - - -
365S GLN* 1.3 79.6 - - - +
367S VAL* 1.3 66.5 + - - +
369S THR* 3.0 21.1 - - - +
370S GLY* 3.3 5.4 + - - -
371S ASN 4.3 6.5 + - - +
374S LYS* 4.0 15.3 - - + +
375S PHE* 3.8 37.7 - - + +
378S VAL* 4.2 2.9 - - + -
402S VAL* 4.7 3.0 - - - +
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Residues in contact with VAL 367 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337S LEU* 3.7 38.4 - - + +
342S ILE* 5.2 3.1 - - + -
363S LEU 2.9 24.7 + - - +
364S THR 4.2 0.7 - - - +
366S ALA* 1.3 78.3 - - - +
368S ARG* 1.3 63.6 + - - +
370S GLY* 3.5 9.0 + - - -
375S PHE* 4.4 7.4 - - + -
398S LEU* 4.1 24.9 - - + -
401S ASN* 5.1 7.4 - - + +
402S VAL* 3.9 36.9 - - + +
405S THR* 4.4 8.7 - - - +
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Residues in contact with ARG 368 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336R ARG* 6.3 1.2 - - - +
342S ILE* 3.5 44.1 - - + +
364S THR* 2.9 18.5 + - + +
365S GLN* 4.4 10.5 + - - +
367S VAL* 1.3 78.9 - - - +
369S THR* 1.3 71.3 + - - +
370S GLY 3.5 0.2 + - - -
405S THR* 3.7 15.5 - - - +
409S MET* 6.1 0.3 - - - +
43Y TRP* 2.8 55.9 + - - +
44Y ASP* 4.6 8.3 + - - +
47Y ASN* 3.4 32.3 - - - +
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Residues in contact with THR 369 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365S GLN 3.1 19.5 + - - +
366S ALA* 3.0 17.9 - - - +
368S ARG* 1.3 89.4 - - - +
370S GLY* 1.3 71.1 + - - +
371S ASN* 3.4 23.0 + - - +
374S LYS* 4.6 12.9 + - + +
405S THR* 5.0 1.0 - - - +
406S GLY* 4.8 0.7 - - - -
409S MET* 4.1 20.1 - - - +
47Y ASN* 4.7 15.6 + - - +
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Residues in contact with GLY 370 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366S ALA 3.3 4.9 + - - -
367S VAL 4.1 5.8 - - - -
368S ARG 3.4 1.8 - - - -
369S THR* 1.3 86.0 - - - +
371S ASN* 1.3 62.8 + - - +
402S VAL 3.5 22.2 - - - -
405S THR 4.9 0.2 - - - -
406S GLY* 3.9 20.2 - - - -
409S MET* 4.9 4.2 - - - +
425S LYS 4.3 3.1 - - - +
426S LEU* 4.0 10.0 - - - +
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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