Contacts of the helix formed by residues 317 - 329 (chain C) in PDB entry 4BZ5
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 SER 317 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255C ASP* 3.5 11.4 + - - -
298C THR* 2.7 27.2 + - - -
299C ASN* 3.7 2.5 - - - -
300C PHE 2.9 27.9 + - - -
315C SER 3.8 1.2 + - - -
316C LEU* 1.3 73.2 - - - +
318C GLY* 1.3 63.4 + - - +
319C TYR* 3.2 17.2 + - - +
320C LEU* 3.2 21.5 + - - +
321C TYR* 2.9 21.5 + - - +
349C LEU* 4.3 0.2 - - - +
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Residues in contact with GLY 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ASP* 2.9 22.9 + - - -
258C TRP* 3.2 27.9 - - - -
259C SER* 3.5 20.3 + - - -
297C LEU* 4.5 2.7 - - - +
316C LEU 3.2 1.8 + - - -
317C SER* 1.3 71.0 + - - +
319C TYR* 1.3 61.6 + - - +
321C TYR* 3.3 2.6 + - - +
322C ALA* 3.0 19.1 + - - +
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Residues in contact with TYR 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 4.2 21.9 - - + +
258C TRP* 3.8 8.6 - + - -
282C CYS* 3.7 26.9 - - - -
283C GLY 2.6 30.1 + - - -
284C ALA* 3.3 6.5 - - - -
286C CYS* 3.0 35.7 + - + +
287C LEU* 3.9 14.8 - - + -
297C LEU* 3.8 19.3 - - + +
298C THR 4.2 9.2 - - - -
317C SER* 3.2 6.5 + - - +
318C GLY* 1.3 76.4 - - - +
320C LEU* 1.3 57.4 + - + +
322C ALA* 3.3 3.6 + - - +
323C ILE* 3.0 34.8 + - - +
349C LEU* 3.6 35.2 - - + -
353C VAL* 5.0 2.2 - - + -
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ASN 3.8 9.6 - - - +
300C PHE 3.7 12.3 - - - +
301C TYR* 3.7 38.1 - - + -
316C LEU* 3.9 9.6 - - + -
317C SER* 3.1 18.2 + - - +
319C TYR* 1.3 77.6 - - + +
321C TYR* 1.3 60.7 + - - +
323C ILE* 4.6 2.9 - - + +
324C LYS* 2.9 33.6 + - - +
349C LEU* 4.9 3.8 - - + +
352C ARG* 3.9 10.5 - - + -
353C VAL* 3.8 40.2 - - + +
356C LEU* 3.6 23.6 - - + +
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Residues in contact with TYR 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C SER* 3.5 48.4 + - - +
260C ASN* 5.0 6.4 + - - -
262C ILE* 5.6 1.3 - - + -
263C GLY* 4.1 8.1 - - - -
264C PRO* 5.6 1.0 - - - +
266C LEU* 6.4 0.2 - - + -
316C LEU* 3.7 23.6 - - + +
317C SER 2.9 13.4 + - - +
318C GLY 3.4 8.7 - - - +
320C LEU* 1.3 77.3 - - - +
322C ALA* 1.3 63.7 + - + +
324C LYS* 3.5 4.3 + - + +
325C LYS* 3.0 63.4 + - + +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 4.2 14.4 - - + -
258C TRP* 4.1 4.0 - - + -
262C ILE* 3.9 27.4 - - + -
266C LEU* 4.3 10.0 - - + +
318C GLY 3.0 17.0 + - - +
319C TYR 3.7 3.6 - - - +
321C TYR* 1.3 81.2 - - + +
323C ILE* 1.3 60.4 + - - +
325C LYS* 3.3 5.3 + - - +
326C ILE* 2.9 36.0 + - + +
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Residues in contact with ILE 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 4.4 4.9 - - + -
280C VAL* 4.0 30.7 - - + -
282C CYS* 4.2 19.3 - - - -
319C TYR 3.0 22.5 + - - +
320C LEU* 4.1 4.7 - - + +
322C ALA* 1.3 73.2 - - - +
324C LYS* 1.3 66.2 + - - +
326C ILE* 3.3 5.2 + - + +
327C LEU* 2.9 45.1 + - + +
335C ILE* 4.2 20.6 - - + -
353C VAL* 4.3 17.0 - - + -
356C LEU* 4.2 7.9 - - + -
357C THR* 4.2 11.0 - - - +
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Residues in contact with LYS 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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301C TYR* 3.1 37.3 + - - -
316C LEU* 4.4 14.3 - - + +
320C LEU 2.9 18.1 + - - +
321C TYR* 3.8 4.9 - - + +
323C ILE* 1.3 78.3 - - - +
325C LYS* 1.3 63.5 + - - +
327C LEU* 3.3 4.3 + - - +
328C SER* 3.0 23.7 + - - -
356C LEU* 4.0 20.4 - - + +
360C GLU* 3.8 30.3 - - - +
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Residues in contact with LYS 325 (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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263C GLY* 3.4 24.5 - - - +
266C LEU* 4.3 11.0 - - + -
267C ASP* 2.8 40.1 + - - +
321C TYR* 3.0 53.3 + - + +
322C ALA* 3.6 5.8 - - - +
323C ILE 3.2 0.2 - - - -
324C LYS* 1.3 76.8 - - - +
326C ILE* 1.3 63.2 + - - +
328C SER* 2.6 27.9 + - - +
329C TRP* 3.4 14.5 + - + +
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Residues in contact with ILE 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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183C VAL* 4.3 20.2 - - + -
185C LEU* 5.2 0.4 - - + -
266C LEU* 4.4 11.4 - - + -
278C VAL* 3.9 23.6 - - + -
280C VAL* 3.8 34.3 - - + -
322C ALA* 2.9 27.1 + - + +
323C ILE* 3.8 7.6 - - + +
325C LYS* 1.3 75.0 - - - +
327C LEU* 1.3 65.0 + - + +
329C TRP* 3.2 50.1 + - + +
330C LYS 4.3 0.9 + - - -
331C VAL* 5.1 1.7 + - - +
333C THR* 4.3 17.1 + - + +
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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
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132C VAL* 3.7 35.0 - - + -
323C ILE* 2.9 38.1 + - + +
324C LYS 3.8 3.6 - - - +
326C ILE* 1.3 78.7 - - + +
328C SER* 1.3 61.0 + - - +
329C TRP 3.0 0.7 - - - -
330C LYS* 3.1 23.8 + - - +
331C VAL 5.8 1.3 - - - +
333C THR* 4.5 17.7 - - + +
335C ILE* 4.7 3.8 - - + -
356C LEU* 4.0 3.6 - - + -
357C THR* 3.8 31.2 - - + +
360C GLU* 4.0 23.5 - - + -
361C VAL* 4.4 6.0 - - + +
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Residues in contact with SER 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ASP* 5.3 0.3 + - - -
324C LYS* 3.0 14.0 + - - -
325C LYS* 2.6 24.4 + - - +
327C LEU* 1.3 76.1 - - - +
329C TRP* 1.3 70.1 + - - +
330C LYS* 3.1 22.8 + - - +
360C GLU* 5.9 2.9 + - - -
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Residues in contact with TRP 329 (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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181C LEU* 4.0 21.8 - - + -
183C VAL* 5.6 0.2 - - + -
266C LEU* 3.2 52.5 - - + -
267C ASP* 3.0 21.1 + - - -
270C ASN* 3.3 43.1 + - + +
278C VAL* 4.1 22.0 - - + -
325C LYS* 3.4 17.0 + - + -
326C ILE* 3.4 36.3 - - + +
327C LEU 3.0 0.4 - - - -
328C SER* 1.3 81.8 + - - +
330C LYS* 1.3 69.2 + - - +
331C VAL* 3.3 15.6 + - + +
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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