Contacts of the helix formed by residues 323 - 341 (chain C) in PDB entry 3LLK
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 323 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321C VAL* 3.7 26.4 + - - +
322C LEU* 1.3 76.4 - - - +
324C GLY* 1.3 72.2 + - - +
325C GLN 3.4 0.2 + - - -
326C ARG* 3.3 13.7 + - - +
327C LEU* 3.2 16.6 + - - +
364C ASN* 4.1 7.2 + - - +
365C LYS* 3.5 36.7 - - + +
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Residues in contact with GLY 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C GLU* 1.3 78.3 - - - +
325C GLN* 1.3 65.7 + - - -
327C LEU* 3.2 3.8 + - - +
328C VAL* 3.2 27.0 + - - +
364C ASN* 4.5 12.2 + - - +
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Residues in contact with GLN 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C GLU 3.4 0.4 + - - -
324C GLY* 1.3 70.4 - - - -
326C ARG* 1.3 60.9 + - - +
328C VAL* 3.1 23.9 + - - +
329C ALA* 2.8 31.9 + - - +
445C TYR* 3.2 36.7 + - + +
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Residues in contact with ARG 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C PHE* 3.2 55.4 - - - -
321C VAL 5.0 5.5 + - - -
322C LEU* 4.3 9.2 - - + -
323C GLU* 3.3 11.6 + - - +
325C GLN* 1.3 77.8 - - - +
327C LEU* 1.3 57.5 + - - +
329C ALA* 3.5 0.5 + - - +
330C LEU 3.0 21.5 + - - -
444C HIS 5.1 0.8 + - - -
445C TYR* 3.0 57.5 + - + +
446C PHE* 3.3 27.0 - - + -
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Residues in contact with LEU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C LEU* 3.9 23.8 - - + +
323C GLU* 3.2 16.8 + - - +
324C GLY 3.2 10.0 + - - +
325C GLN 3.1 0.6 - - - -
326C ARG* 1.3 77.6 - - - +
328C VAL* 1.3 60.6 + - + +
330C LEU* 3.2 16.8 + - + +
331C LYS* 2.9 48.3 + - + +
358C LEU* 4.8 1.6 - - + -
363C ARG 4.6 3.1 - - - +
364C ASN* 3.5 26.5 - - - +
366C ILE* 3.9 31.6 - - + -
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Residues in contact with VAL 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C GLY 3.2 16.5 + - - +
325C GLN* 3.1 29.3 + - - +
327C LEU* 1.3 77.7 - - + +
329C ALA* 1.3 62.7 + - - +
331C LYS* 3.3 9.6 + - + +
332C LYS* 2.9 50.8 + - + +
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Residues in contact with ALA 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C GLN* 2.8 16.6 + - - +
326C ARG 3.5 5.2 - - - +
328C VAL* 1.3 77.3 - - - +
330C LEU* 1.3 57.7 - - - +
332C LYS* 3.2 8.6 + - - +
333C PHE* 2.9 31.8 + - - +
438C ALA 5.1 1.9 - - - +
441C GLY* 3.9 20.6 - - - +
442C TYR* 5.4 0.6 + - - -
445C TYR* 3.6 26.2 - - + -
446C PHE* 4.5 3.8 - - + -
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C ILE* 5.9 1.3 - - + -
312C LEU* 5.8 1.3 - - + -
316C VAL* 3.8 32.3 - - + -
322C LEU* 3.6 31.2 - - + -
326C ARG 3.0 14.5 + - - +
327C LEU* 3.4 18.8 - - + +
329C ALA* 1.3 76.8 - - - +
331C LYS* 1.3 57.9 + - - +
333C PHE* 3.8 6.8 - - + +
334C VAL* 2.9 50.5 + - + +
358C LEU* 4.6 13.9 - - + -
371C PHE* 4.7 9.6 - - + -
442C TYR* 5.7 3.1 - - + -
446C PHE* 3.7 17.2 - - + -
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Residues in contact with LYS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C LEU* 2.9 43.3 + - + +
328C VAL* 3.7 10.1 - - + +
330C LEU* 1.3 75.4 - - - +
332C LYS* 1.3 64.5 + - + +
334C VAL* 3.9 1.0 - - - +
335C ALA* 3.0 25.9 + - - +
355C ASN* 4.3 3.6 + - - +
358C LEU* 3.1 51.8 + - + +
359C LYS* 4.6 10.4 + - + +
361C GLN 3.4 17.1 + - - -
366C ILE* 5.0 3.4 - - - -
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Residues in contact with LYS 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C VAL* 2.9 43.7 + - + +
329C ALA* 3.5 8.7 - - - +
331C LYS* 1.3 78.3 - - + +
333C PHE* 1.3 63.5 + - - +
335C ALA* 3.3 6.4 + - - +
336C VAL* 3.1 24.8 + - - +
434C GLU* 4.3 21.6 + - + +
438C ALA* 4.2 18.6 - - + -
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Residues in contact with PHE 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C ILE* 4.0 19.1 - - + -
329C ALA 2.9 19.9 + - - +
330C LEU* 3.8 8.1 - - + +
332C LYS* 1.3 74.6 - - - +
334C VAL* 1.3 61.5 + - + +
336C VAL* 3.0 7.7 + - + +
337C LEU* 2.9 57.2 + - + +
410C LEU* 4.4 7.0 - - + -
411C PHE* 3.6 34.8 - + - -
414C LEU* 4.2 15.3 - - + -
438C ALA* 3.8 30.9 - - + +
439C ILE* 4.5 6.1 - - + -
442C TYR* 3.7 34.8 - + + -
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Residues in contact with VAL 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LEU* 5.1 10.5 - - + -
330C LEU* 2.9 35.4 + - + +
331C LYS 3.9 2.0 - - - +
333C PHE* 1.3 77.0 - - + +
335C ALA* 1.3 62.3 + - - +
337C LEU* 3.1 17.8 + - + +
338C ALA* 2.9 22.3 + - - +
351C LEU* 4.5 7.0 - - + +
354C VAL* 4.3 11.7 - - + -
355C ASN* 3.6 34.3 - - + +
358C LEU* 3.7 22.9 - - + -
371C PHE* 5.5 0.9 - - + -
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Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C LYS 3.0 18.5 + - - +
332C LYS* 3.5 8.1 - - - +
334C VAL* 1.3 76.5 - - - +
336C VAL* 1.3 63.2 + - + +
338C ALA* 3.5 2.9 + - - +
339C LYS* 3.2 22.7 + - - +
355C ASN* 3.4 22.5 - - - +
359C LYS* 6.1 1.1 - - + -
434C GLU* 6.1 1.1 - - - +
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Residues in contact with VAL 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C LYS 3.1 13.1 + - - +
333C PHE* 3.0 11.1 + - + +
335C ALA* 1.3 79.0 - - + +
337C LEU* 1.3 53.6 + - - +
339C LYS* 3.3 2.0 + - - -
340C TYR* 2.8 53.2 + - + +
414C LEU* 4.0 26.7 - - + -
431C LYS 5.4 1.6 - - - +
434C GLU* 3.9 20.4 - - + +
435C VAL* 4.4 15.3 - - + +
438C ALA* 3.5 23.8 - - + -
439C ILE* 6.0 0.4 - - + -
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Residues in contact with LEU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C LEU* 3.9 32.1 - - + -
311C ILE* 5.5 5.2 - - + -
312C LEU* 5.6 7.2 - - + -
333C PHE* 2.9 42.1 + - + +
334C VAL* 3.4 19.3 - - + +
336C VAL* 1.3 76.9 - - - +
338C ALA* 1.3 61.5 + - - +
341C PHE* 2.8 39.1 + - + +
348C GLN* 3.6 1.6 + - - -
351C LEU* 3.9 20.6 - - + -
410C LEU* 4.1 19.3 - - + -
414C LEU* 4.2 12.8 - - + -
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Residues in contact with ALA 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C VAL 2.9 15.9 + - - +
335C ALA 3.8 4.9 - - - +
337C LEU* 1.3 76.3 - - - +
339C LYS* 1.3 56.7 + - - +
348C GLN* 2.7 22.7 + - - +
351C LEU* 3.9 25.0 - - - +
352C HIS* 4.2 9.7 - - + +
355C ASN* 4.0 26.0 - - + +
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Residues in contact with LYS 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C ALA 3.2 14.3 + - - +
336C VAL* 4.0 1.8 - - - +
337C LEU 3.1 0.6 - - - -
338C ALA* 1.3 83.3 - - + +
340C TYR* 1.3 99.1 + - + +
341C PHE 4.9 0.3 - - - +
348C GLN* 4.6 2.7 + - - -
417C GLN* 5.6 0.5 + - - -
421C GLN* 4.3 21.9 - - - +
431C LYS* 2.8 40.0 - - - +
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Residues in contact with TYR 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C VAL* 2.8 30.3 + - + +
339C LYS* 1.3 123.2 + - + +
341C PHE* 1.3 66.9 + - - +
342C PRO* 3.2 1.0 - - - +
414C LEU* 3.7 19.1 - - + +
417C GLN* 2.9 40.7 + - + +
418C ALA* 3.4 30.5 - - + -
421C GLN* 3.9 21.0 - - + +
431C LYS 3.8 14.6 - - - -
432C ALA* 3.3 20.3 + - - +
435C VAL* 3.9 20.9 - - + -
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Residues in contact with PHE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C MET* 4.9 4.5 - - - -
304C LEU* 3.8 33.9 - - + -
305C GLU* 4.4 5.6 - - + -
308C LEU* 3.4 42.0 - - + -
337C LEU* 2.8 29.5 + - + +
339C LYS 4.9 0.3 - - - +
340C TYR* 1.3 72.1 - - - +
342C PRO* 1.3 70.3 - - + +
343C GLY* 3.1 38.6 - - - -
347C VAL* 3.9 7.0 - - + -
348C GLN* 3.0 25.7 + - - +
351C LEU* 3.6 17.9 - - + -
410C LEU* 3.6 27.6 - - + -
414C LEU* 3.6 7.0 - - - +
417C GLN* 4.1 1.9 + - - -
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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
------------------------------------------------------------
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