Contacts of the helix formed by residues 343 - 357 (chain Z) in PDB entry 5LN3
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 LYS 343 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309Z GLU* 3.5 44.2 + - + +
310Z ASP* 3.5 24.3 + - - -
337Z LEU* 6.3 0.8 - - - +
338Z ASP* 3.4 33.7 + - - +
341Z GLU* 4.6 7.3 + - - +
342Z PRO* 1.3 76.6 - - - +
344Z VAL* 1.3 69.9 - - + +
345Z PRO 3.4 0.2 - - - -
346Z ASP* 3.3 6.1 + - - +
347Z ASP* 2.9 39.7 + - - +
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Residues in contact with VAL 344 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296Z PHE* 6.1 1.3 - - + -
338Z ASP* 4.3 14.2 + - + +
339Z ILE* 5.0 5.2 - - + -
343Z LYS* 1.3 85.0 - - + +
345Z PRO* 1.3 71.9 - - + +
347Z ASP* 3.4 11.3 + - + +
348Z ILE* 3.0 26.5 + - + +
833Z PHE* 5.1 16.8 - - + -
836Z GLU 5.4 0.9 - - - +
837Z LEU* 3.8 33.9 - - + -
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Residues in contact with PRO 345 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296Z PHE* 4.4 16.6 - - + +
299Z GLY* 4.7 9.6 - - - +
338Z ASP 4.3 5.6 - - - +
339Z ILE* 4.3 26.9 - - + +
342Z PRO* 4.0 24.2 - - + -
343Z LYS 4.0 1.8 - - - +
344Z VAL* 1.3 94.7 - - + +
346Z ASP* 1.3 58.8 + - - +
348Z ILE* 3.3 10.8 - - + +
349Z TYR* 3.2 50.7 + - + +
897Z PHE* 6.2 0.7 - - + -
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Residues in contact with ASP 346 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307Z LEU* 5.5 4.5 - - + +
309Z GLU* 2.9 23.1 - - - +
342Z PRO* 4.1 19.0 - - + +
343Z LYS 3.4 8.0 - - - +
345Z PRO* 1.3 75.0 - - - +
347Z ASP* 1.3 68.2 + - - +
349Z TYR* 3.7 12.8 + - - +
350Z LYS* 3.3 23.9 + - - +
420Z TRP* 3.9 34.6 - - - +
454Z GLY 4.7 7.8 - - - +
455Z VAL* 5.0 6.0 - - - +
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Residues in contact with ASP 347 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309Z GLU* 4.9 2.5 - - - +
343Z LYS* 2.9 33.3 + - - +
344Z VAL* 3.6 12.0 - - + +
346Z ASP* 1.3 84.9 - - - +
348Z ILE* 1.3 57.8 + - + +
350Z LYS* 3.3 27.1 + - - +
351Z THR* 3.1 31.7 + - - +
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Residues in contact with ILE 348 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344Z VAL* 3.0 16.6 + - + +
345Z PRO* 3.3 17.0 + - + +
347Z ASP* 1.3 74.7 - - + +
349Z TYR* 1.4 78.7 + - + +
351Z THR* 3.3 12.9 + - + +
352Z HIS* 2.7 54.0 + - + +
831Z VAL* 5.1 6.1 - - + -
833Z PHE* 4.4 26.9 - - + -
876Z HIS* 4.3 17.9 - - + +
897Z PHE* 5.3 1.6 - - + -
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Residues in contact with TYR 349 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296Z PHE* 5.6 0.9 + - - -
299Z GLY 5.7 0.7 - - - -
300Z ARG* 4.2 22.0 - - - +
345Z PRO* 3.2 37.7 + - + +
346Z ASP* 4.0 9.6 - - - +
347Z ASP 3.4 0.2 - - - -
348Z ILE* 1.4 88.1 - - + +
350Z LYS* 1.4 63.7 + - - +
352Z HIS* 3.5 3.7 + - - -
353Z LEU* 3.1 32.8 + - + +
420Z TRP* 6.6 0.2 - - + -
775Z THR* 3.4 12.5 - - + +
776Z LEU* 4.8 8.7 - - + -
827Z PRO* 3.5 30.7 - - + -
829Z MET* 4.0 14.8 - - - -
897Z PHE* 3.8 35.4 - + - -
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Residues in contact with LYS 350 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346Z ASP* 3.3 13.6 + - - +
347Z ASP* 3.3 33.8 + - - +
348Z ILE 3.3 0.4 - - - -
349Z TYR* 1.4 77.6 - - - +
351Z THR* 1.4 62.2 + - - +
353Z LEU* 3.2 14.6 + - - +
354Z GLU* 3.1 40.1 + - + +
384Z ALA* 5.0 1.3 - - + +
419Z LEU 5.7 0.9 - - - +
420Z TRP* 4.0 36.2 + - + +
421Z ASP* 3.5 28.1 + - - +
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Residues in contact with THR 351 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347Z ASP* 3.1 15.4 + - - +
348Z ILE* 3.3 17.4 + - + +
350Z LYS* 1.4 75.4 - - - +
352Z HIS* 1.3 56.4 + - + +
354Z GLU* 3.3 16.3 + - + +
355Z ASN* 3.0 49.7 + - - +
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Residues in contact with HIS 352 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348Z ILE* 2.7 43.8 + - + +
349Z TYR* 3.6 3.8 - - - +
350Z LYS 3.3 0.2 - - - -
351Z THR* 1.3 75.3 - - + +
353Z LEU* 1.4 62.3 + - - +
355Z ASN* 3.8 11.3 + - - +
356Z ASN* 3.1 30.5 + - - +
775Z THR* 3.2 23.6 - - + +
829Z MET* 3.4 32.0 - - + +
831Z VAL* 4.1 3.0 - - - +
876Z HIS* 3.3 32.7 + - + +
877Z GLY* 3.6 25.9 + - - -
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Residues in contact with LEU 353 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349Z TYR* 3.1 24.1 + - + +
350Z LYS* 3.2 7.8 + - - +
352Z HIS* 1.4 60.1 - - - +
354Z GLU* 1.3 61.0 + - - +
356Z ASN* 5.0 0.9 - - - -
357Z ARG* 3.3 19.6 + - - -
383Z ALA* 6.3 2.7 - - + -
384Z ALA* 3.5 20.2 - - + +
420Z TRP* 3.8 35.0 - - + +
771Z LEU* 6.5 0.7 - - + -
772Z GLY 3.4 25.4 - - - +
773Z LYS* 4.0 20.7 + - + +
775Z THR* 3.7 15.5 - - + +
776Z LEU* 4.2 22.7 - - + -
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Residues in contact with GLU 354 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350Z LYS* 3.1 32.4 + - + +
351Z THR* 3.3 19.8 + - + +
353Z LEU* 1.3 75.6 - - - +
355Z ASN* 1.4 63.0 + - - +
357Z ARG* 3.2 28.1 + - - +
384Z ALA* 4.4 4.0 - - + -
385Z PHE* 3.9 50.7 - - + +
421Z ASP* 4.8 11.3 - - - +
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Residues in contact with ASN 355 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351Z THR* 3.0 43.0 + - - +
352Z HIS* 3.8 13.7 + - - +
354Z GLU* 1.4 75.2 - - - +
356Z ASN* 1.3 71.3 + - - +
357Z ARG* 3.6 10.3 + - - +
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Residues in contact with ASN 356 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352Z HIS 3.1 15.6 + - - +
353Z LEU 4.3 1.8 - - - +
354Z GLU 3.5 0.4 - - - -
355Z ASN* 1.3 87.3 - - - +
357Z ARG* 1.4 73.2 + - - +
773Z LYS* 3.0 32.0 + - + +
774Z GLY 4.8 0.4 - - - -
775Z THR* 3.6 18.2 + - - +
877Z GLY* 4.5 12.0 - - - -
878Z GLU* 4.4 15.0 + - - +
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Residues in contact with ARG 357 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353Z LEU 3.3 11.9 + - - -
354Z GLU 3.2 24.1 + - - +
355Z ASN* 3.6 8.3 + - - +
356Z ASN* 1.4 88.2 - - - +
358Z PHE* 1.4 70.7 + - - +
359Z GLY 5.0 0.4 - - - +
384Z ALA 5.6 1.1 - - - -
385Z PHE* 3.6 45.9 - - + -
387Z GLN* 4.3 11.6 - - - +
773Z LYS* 3.9 23.4 - - - +
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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