Contacts of the helix formed by residues 344 - 357 (chain Z) 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 VAL 344 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300Z ARG* 5.9 3.4 - - - +
304Z PHE* 4.3 13.0 - - + -
338Z ASP* 3.2 25.4 + - + +
339Z ILE* 4.8 7.4 - - + -
343Z LYS* 1.3 75.7 - - - +
345Z PRO* 1.3 74.5 - - + +
346Z ASP 3.2 0.2 - - - -
347Z ASP* 2.9 23.3 + - + +
348Z ILE* 3.1 17.3 + - + +
818Z LEU* 4.1 26.0 - - + -
898Z VAL 5.7 0.9 - - - +
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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
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304Z PHE* 5.4 7.6 - - + -
307Z LEU* 4.4 18.4 - - + -
338Z ASP 4.4 2.2 - - - +
339Z ILE* 5.0 6.1 - - + +
342Z PRO* 3.5 36.1 - - + -
343Z LYS 3.7 0.2 - - - +
344Z VAL* 1.3 96.2 - - + +
346Z ASP* 1.3 57.0 + - - +
348Z ILE* 3.2 15.6 + - + +
349Z TYR* 2.9 54.7 + - + +
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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
----------------------------------------------------------
342Z PRO* 2.8 23.4 - - - +
343Z LYS* 3.6 12.6 + - - +
344Z VAL 3.2 1.0 - - - -
345Z PRO* 1.3 78.9 - - - +
347Z ASP* 1.3 63.7 + - - +
349Z TYR* 4.1 7.2 - - - +
350Z LYS* 3.8 16.3 + - - +
385Z PHE* 4.1 12.0 - - + -
420Z TRP* 3.4 36.2 - - - +
422Z VAL* 3.7 24.2 - - + +
454Z GLY* 3.5 14.3 - - - +
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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
----------------------------------------------------------
343Z LYS 3.2 17.5 - - - +
344Z VAL* 2.9 16.7 + - + +
346Z ASP* 1.3 80.6 - - - +
348Z ILE* 1.3 60.4 + - - +
349Z TYR 3.5 0.2 - - - -
350Z LYS* 3.4 6.9 + - - +
351Z THR* 3.0 26.7 + - - -
898Z VAL* 3.6 30.0 - - + +
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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
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304Z PHE* 6.1 0.7 - - + -
344Z VAL* 3.5 15.0 - - + +
345Z PRO* 3.3 23.3 - - + +
347Z ASP* 1.3 75.0 - - - +
349Z TYR* 1.3 70.9 + - + +
350Z LYS 3.1 0.9 - - - -
351Z THR* 3.5 6.0 - - - -
352Z HIS* 2.9 42.3 + - + +
805Z ASP* 5.1 1.6 - - - +
809Z ILE* 3.5 32.8 - - + -
818Z LEU* 3.9 22.4 - - + -
897Z PHE* 3.9 19.3 - - + -
898Z VAL 3.7 17.5 - - - +
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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
----------------------------------------------------------
342Z PRO* 6.0 0.7 - - + -
345Z PRO* 2.9 45.8 + - + +
346Z ASP* 4.1 3.8 - - - +
348Z ILE* 1.3 78.2 - - + +
350Z LYS* 1.3 58.1 + - - +
352Z HIS* 3.2 13.5 + + - +
353Z LEU* 3.0 23.2 + - - +
384Z ALA 4.7 1.3 - - - +
385Z PHE* 3.9 26.0 - - + +
420Z TRP* 3.3 59.3 - + + -
759Z LEU* 3.6 23.4 - - + +
760Z PHE* 5.9 0.7 - + - -
804Z LEU* 5.3 0.5 - - - -
805Z ASP* 3.4 44.2 + - + +
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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
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346Z ASP 3.8 9.7 + - - +
347Z ASP* 3.4 10.5 + - - +
348Z ILE 3.1 0.6 - - - -
349Z TYR* 1.3 76.4 - - - +
351Z THR* 1.3 61.8 + - - +
353Z LEU* 3.1 12.6 + - + +
354Z GLU* 2.9 63.1 + - + +
385Z PHE* 3.2 37.9 - - + -
387Z GLN* 5.3 4.0 - - - +
898Z VAL* 6.1 3.6 - - + -
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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
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347Z ASP 3.0 15.9 + - - -
348Z ILE* 3.2 13.9 + - - -
350Z LYS* 1.3 74.1 - - - +
352Z HIS* 1.3 65.7 + - - +
354Z GLU* 3.2 6.3 + - + +
355Z ASN* 2.9 37.2 + - - +
896Z GLY 3.2 27.1 - - - +
897Z PHE* 3.8 21.8 - - + -
898Z VAL* 3.3 27.1 + - + +
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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* 2.9 45.9 + - + +
349Z TYR* 3.3 15.6 - - - +
351Z THR* 1.3 74.6 - - - +
353Z LEU* 1.3 57.6 + - - +
355Z ASN* 4.6 1.6 - - - +
356Z ASN* 2.9 42.2 + - - +
357Z ARG 3.9 0.3 + - - -
358Z PHE* 4.6 3.4 - - - -
759Z LEU* 3.8 21.5 - - + +
805Z ASP* 3.4 29.1 + - - -
807Z ARG* 3.5 36.4 + - + +
808Z ASN 5.4 0.4 + - - -
809Z ILE* 4.8 3.8 - - + +
849Z ALA* 6.2 0.4 - - + -
897Z PHE* 3.7 28.7 - + - -
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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
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349Z TYR 3.0 10.4 + - - +
350Z LYS* 3.1 16.8 + - - +
352Z HIS* 1.3 77.1 - - - +
354Z GLU* 1.3 76.5 + - - +
357Z ARG* 2.9 38.5 + - - +
358Z PHE* 3.5 48.6 - - + +
385Z PHE* 3.3 39.5 - - + +
386Z GLY* 4.3 4.0 - - - -
387Z GLN* 4.5 13.5 - - + +
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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* 2.9 57.0 + - + +
351Z THR* 3.2 6.0 + - - +
353Z LEU* 1.3 91.7 - - - +
355Z ASN* 1.3 68.7 + - - +
357Z ARG* 3.3 41.1 + - - +
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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
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351Z THR* 2.9 37.7 + - - +
352Z HIS* 4.5 2.2 - - - +
354Z GLU* 1.3 89.4 - - - +
356Z ASN* 1.3 69.4 + - - +
357Z ARG* 3.5 1.7 - - - +
849Z ALA* 5.6 7.1 - - + +
896Z GLY* 3.6 14.6 + - - +
897Z PHE* 4.7 8.1 - - - -
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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
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352Z HIS* 2.9 22.4 + - - +
355Z ASN* 1.3 83.5 - - - +
357Z ARG* 1.3 74.1 + - - +
358Z PHE* 4.5 7.7 - - + -
757Z ASN* 3.4 27.9 + - + +
807Z ARG* 3.1 40.0 - - - +
849Z ALA* 4.2 19.0 + - - +
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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* 2.9 42.6 + - - +
354Z GLU* 3.3 49.0 + - - +
355Z ASN 3.5 3.1 - - - +
356Z ASN* 1.3 87.3 - - - +
358Z PHE* 1.3 77.6 + - - +
359Z GLY* 4.3 0.8 + - - +
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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