Contacts of the helix formed by residues 320 - 336 (chain C) in PDB entry 3EZZ
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 ASN 320 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249C ASP* 3.3 30.4 + - - +
250C ASN 2.9 26.7 + - - +
251C HIS* 3.8 13.9 - - + +
285C SER* 3.1 10.9 + - - +
318C SER* 3.2 5.2 + - - +
319C PRO* 1.3 74.6 - - - +
321C PHE* 1.3 63.7 + - + +
322C SER* 3.0 26.9 + - - -
323C PHE* 2.9 28.4 + - - +
324C MET 3.0 4.7 + - - -
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Residues in contact with PHE 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C HIS* 4.6 16.1 + - + -
319C PRO 5.0 2.9 - - - -
320C ASN* 1.3 72.3 - - + +
322C SER* 1.3 65.2 - - - +
324C MET* 2.8 25.5 + - + +
325C GLY* 2.8 12.5 + - - -
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Residues in contact with SER 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ASN 3.8 2.2 + - - -
251C HIS* 2.9 46.6 + - - -
320C ASN* 3.0 15.9 + - - -
321C PHE* 1.3 74.5 - - - +
323C PHE* 1.3 63.9 + - - +
325C GLY* 3.0 9.4 + - - -
326C GLN* 2.8 40.9 + - - +
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Residues in contact with PHE 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C VAL* 4.3 5.2 - - + -
248C GLU 3.2 23.8 - - - -
249C ASP* 3.7 0.2 - - - -
250C ASN 3.0 17.9 - - - -
253C ALA* 3.5 21.3 - - + -
255C ILE* 4.0 13.7 - - + -
285C SER* 3.4 14.1 - - - -
286C ARG* 3.5 28.3 - - + -
289C THR* 3.2 32.9 - - + +
319C PRO* 4.2 3.8 - - + -
320C ASN* 2.9 24.3 + - - +
322C SER* 1.3 73.8 - - - +
324C MET* 1.3 54.1 + - - +
326C GLN* 3.2 16.9 + - - +
327C LEU* 2.7 39.8 + - - +
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Residues in contact with MET 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C LEU* 3.9 16.2 - - + +
307C PHE* 4.0 20.6 - - + -
318C SER* 4.7 0.7 - - - +
319C PRO* 2.9 56.5 - - + +
320C ASN 3.0 4.2 + - - -
321C PHE* 2.8 27.9 + - + +
323C PHE* 1.3 77.4 - - - +
325C GLY* 1.3 59.2 + - - +
327C LEU* 3.1 23.3 + - - +
328C LEU* 3.2 21.9 + - + +
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Residues in contact with GLY 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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321C PHE 2.8 12.0 + - - -
322C SER* 3.0 3.3 + - - -
324C MET* 1.3 76.2 - - - +
326C GLN* 1.3 57.1 + - - +
328C LEU* 3.0 17.2 + - - +
329C GLN* 2.9 28.4 + - - +
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Residues in contact with GLN 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C HIS 4.6 1.0 + - - -
253C ALA 2.8 22.7 + - - +
254C ASP* 3.5 4.2 - - - -
255C ILE* 3.2 31.4 + - + +
256C SER* 3.2 28.0 + - - +
259C PHE* 3.9 5.3 - - + -
322C SER* 2.8 36.9 + - - +
323C PHE* 3.6 11.4 - - - +
325C GLY* 1.3 75.9 - - - +
327C LEU* 1.3 57.3 + - - +
329C GLN* 3.5 15.6 + - - +
330C PHE* 3.1 28.8 + - - +
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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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259C PHE* 4.1 7.4 - - + -
289C THR* 3.4 48.0 - - + +
292C LEU* 3.8 24.9 - - + -
293C ALA* 3.8 7.4 - - - +
296C MET* 3.0 45.9 - - + +
303C LEU* 3.9 12.9 - - + +
319C PRO* 4.2 10.3 - - + -
323C PHE 2.7 26.1 + - - +
324C MET* 3.3 14.8 - - - +
325C GLY 3.1 0.2 - - - -
326C GLN* 1.3 73.7 - - - +
328C LEU* 1.3 57.6 + - - +
330C PHE* 4.0 2.4 - - - +
331C GLU* 3.2 13.9 + - - +
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Residues in contact with LEU 328 (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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303C LEU* 3.5 18.2 - - + -
324C MET* 3.2 18.1 + - + +
325C GLY* 3.0 14.5 + - - +
327C LEU* 1.3 75.1 - - - +
329C GLN* 1.3 60.0 + - - +
330C PHE 3.0 1.3 - - - -
331C GLU* 2.6 54.9 + - - +
332C SER* 3.2 6.4 + - - -
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Residues in contact with GLN 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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256C SER* 5.5 7.0 + - - -
325C GLY 2.9 12.5 + - - +
326C GLN* 3.7 19.0 - - - +
328C LEU* 1.3 74.9 - - - +
330C PHE* 1.3 58.0 + - - +
332C SER* 2.7 25.8 + - - -
333C GLN* 3.1 27.3 + - - +
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Residues in contact with PHE 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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256C SER* 5.5 1.6 - - - -
259C PHE* 3.7 31.0 - + + -
260C MET* 4.3 17.5 - - + -
263C ILE* 4.0 21.5 - - + -
293C ALA* 3.3 30.3 - - + -
296C MET* 4.1 18.6 - - + -
297C MET* 4.0 6.3 - - - -
326C GLN 3.1 15.4 + - - +
327C LEU 4.0 2.7 - - - +
328C LEU 3.0 0.4 - - - -
329C GLN* 1.3 78.3 - - - +
331C GLU* 1.3 63.5 + - - +
333C GLN* 3.3 22.4 + - + +
334C VAL* 3.0 48.9 + - + +
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Residues in contact with GLU 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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296C MET* 4.1 17.5 - - - -
301C VAL 4.6 4.3 - - - +
302C ARG* 2.8 35.5 - - - -
303C LEU* 3.3 19.4 + - - +
304C GLU 5.1 0.2 + - - -
327C LEU 3.2 15.2 + - - +
328C LEU* 2.6 44.7 + - - +
330C PHE* 1.3 67.6 - - - +
332C SER* 1.3 65.1 + - - +
334C VAL* 3.1 15.7 + - - +
335C LEU* 3.2 24.8 + - + +
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Residues in contact with SER 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 LEU 3.2 4.6 + - - -
329C GLN* 2.7 25.2 + - - -
331C GLU* 1.3 79.3 - - - +
333C GLN* 1.3 70.4 + - - +
335C LEU* 3.2 9.3 + - - +
336C ALA* 3.1 21.6 + - - +
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Residues in contact with GLN 333 (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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329C GLN* 3.1 42.1 + - - +
330C PHE* 3.3 22.6 + - + +
331C GLU 3.2 0.4 - - - -
332C SER* 1.3 85.0 + - - +
334C VAL* 1.3 63.4 + - - +
336C ALA* 3.2 25.8 + - - +
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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
----------------------------------------------------------
296C MET* 3.4 27.1 - - + +
297C MET* 3.5 37.7 - - + +
300C ARG* 4.6 16.3 + - + -
301C VAL 5.5 0.4 - - - +
330C PHE* 3.0 57.7 + - + +
331C GLU* 3.1 9.1 + - - +
333C GLN* 1.3 75.6 - - - +
335C LEU* 1.3 65.0 + - + +
336C ALA* 4.0 4.7 - - - +
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Residues in contact with LEU 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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300C ARG* 4.8 15.5 + - + +
301C VAL* 4.8 23.6 - - - +
302C ARG* 4.2 23.3 - - + +
331C GLU* 3.2 26.9 + - + +
332C SER* 3.2 10.4 + - - +
334C VAL* 1.3 79.2 - - + +
336C ALA* 1.3 68.4 + - - +
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Residues in contact with ALA 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 SER 3.1 11.9 + - - +
333C GLN* 3.4 20.9 - - - +
334C VAL 4.0 4.2 - - - +
335C LEU* 1.3 83.5 - - - +
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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