Contacts of the helix formed by residues 320 - 336 (chain C) in PDB entry 4EJJ
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 HIS 320 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C LEU* 3.0 11.3 + - + +
317C LEU 3.4 8.9 - - - +
319C LYS* 1.3 107.3 - - + +
321C PRO* 1.4 57.8 - - - +
322C GLU* 3.0 6.7 - - + -
323C VAL* 2.9 42.6 + - + +
324C GLU 3.5 1.0 + - - -
410C ASP* 6.1 0.6 - - - +
411C PHE* 3.6 51.7 + + + +
473C VAL* 6.1 1.1 - - + -
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Residues in contact with PRO 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C LEU 3.8 9.8 - - - +
318C MET* 4.2 6.7 - - - +
319C LYS 3.4 12.6 - - - +
320C HIS* 1.4 80.6 - - - +
322C GLU* 1.3 59.4 + - + +
323C VAL 3.3 0.7 - - - -
324C GLU* 3.9 13.5 - - + +
325C ALA* 3.3 26.7 + - - +
468C PRO* 4.1 23.3 - - + -
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C HIS* 4.6 3.6 - - + +
321C PRO* 1.3 80.9 - - + +
323C VAL* 1.3 62.7 + - + +
324C GLU 3.5 0.2 - - - -
325C ALA* 4.2 5.5 - - - +
326C LYS* 3.5 43.6 + - - +
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Residues in contact with VAL 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C LEU* 5.0 5.4 - - + -
320C HIS* 2.9 33.4 + - + +
322C GLU* 1.3 77.7 - - + +
324C GLU* 1.3 66.0 + - - +
326C LYS* 3.4 3.1 + - - +
327C VAL* 3.1 24.0 + - + +
351C TYR* 3.1 23.8 - - - +
355C VAL* 3.7 22.2 - - + -
411C PHE* 4.3 14.8 - - + -
413C PRO* 3.7 26.5 - - + -
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Residues in contact with GLU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C LEU* 3.9 29.0 + - + +
318C MET* 5.6 1.6 - - - -
320C HIS 3.5 3.0 + - - -
321C PRO* 3.9 15.2 - - - +
323C VAL* 1.3 79.0 - - - +
325C ALA* 1.3 51.3 + - - +
327C VAL* 3.0 8.0 + - - +
328C HIS* 2.8 62.7 + - + +
457C MET* 4.3 11.5 - - - +
461C ARG* 3.4 3.9 - - - +
462C LEU* 3.1 48.8 + - + +
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C PRO 3.3 16.0 + - - +
322C GLU* 4.4 5.6 - - - +
323C VAL 3.4 0.2 - - - -
324C GLU* 1.3 78.8 - - - +
326C LYS* 1.3 56.7 + - - +
328C HIS* 3.8 10.0 - - - +
329C GLU* 3.0 28.8 + - - +
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Residues in contact with LYS 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C GLU* 3.5 29.2 + - - +
323C VAL 3.4 1.3 + - - +
324C GLU 3.2 0.6 - - - -
325C ALA* 1.3 76.1 - - - +
327C VAL* 1.3 62.5 + - - +
329C GLU* 3.8 8.6 - - + +
330C GLU* 3.2 21.8 + - - +
351C TYR* 3.4 45.8 + - + +
414C GLN* 5.2 7.5 + - - -
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Residues in contact with VAL 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C LEU* 5.1 4.9 - - + -
323C VAL 3.1 16.7 + - - +
324C GLU* 3.0 11.8 + - - +
326C LYS* 1.3 75.5 - - - +
328C HIS* 1.3 56.2 + - + +
330C GLU* 2.9 7.8 + - - +
331C ILE* 2.8 55.9 + - + +
351C TYR* 3.9 17.7 - - + -
352C MET* 3.6 28.7 - - + -
355C VAL* 4.1 19.5 - - + -
457C MET* 4.2 15.9 - - + -
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Residues in contact with HIS 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C GLU* 2.8 50.1 + - + +
325C ALA* 3.8 8.9 - - - +
327C VAL* 1.3 78.1 - - + +
329C GLU* 1.3 61.6 + - - +
331C ILE* 3.6 2.8 + - + +
332C ASP* 3.0 30.8 + - - +
457C MET* 2.9 30.4 + - + +
460C PHE 2.8 26.1 + - - -
461C ARG* 3.7 14.3 - - + -
494C ARG* 3.4 29.6 + - - +
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Residues in contact with GLU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C ALA 3.0 19.1 + - - +
326C LYS* 3.8 9.5 - - + +
327C VAL 3.2 0.2 - - - -
328C HIS* 1.3 77.6 - - - +
330C GLU* 1.3 68.5 + - - +
332C ASP* 3.6 5.3 + - - +
333C ARG* 3.1 46.9 + - - +
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Residues in contact with GLU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C LYS 3.2 12.3 + - - +
327C VAL* 2.9 9.5 + - - +
329C GLU* 1.3 79.9 + - - +
331C ILE* 1.3 67.8 + - - +
333C ARG* 3.1 25.7 + - - +
334C VAL* 3.0 31.0 + - + +
349C MET* 3.4 30.8 - - + +
350C PRO* 3.3 10.4 - - - +
351C TYR* 3.1 34.1 + - + +
352C MET* 3.0 22.9 + - - +
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Residues in contact with ILE 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C VAL* 2.8 32.5 + - + +
328C HIS* 3.8 4.9 - - - +
330C GLU* 1.3 71.7 - - - +
332C ASP* 1.3 64.3 + - - +
335C ILE* 3.0 38.0 + - + +
336C GLY 3.4 4.6 + - - +
349C MET* 3.7 24.9 - - + +
352C MET* 3.6 9.6 - - + -
454C THR* 3.8 9.9 - - + +
457C MET* 3.6 33.2 - - + +
458C GLN* 3.6 38.1 - - + +
494C ARG* 4.5 0.7 - - - +
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Residues in contact with ASP 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASP* 5.2 3.3 - - - +
328C HIS 3.0 19.2 + - - +
329C GLU* 3.8 6.8 - - - +
331C ILE* 1.3 77.3 - - - +
333C ARG* 1.3 68.6 + - - +
336C GLY* 3.2 24.0 + - - +
337C LYS* 3.5 23.1 + - - +
458C GLN* 6.0 0.2 - - - +
494C ARG* 2.8 40.3 + - - -
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Residues in contact with ARG 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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155A PHE* 6.2 5.4 - - - -
192A ASP* 4.5 8.8 - - - +
194A LYS* 3.8 27.1 - - - +
329C GLU* 3.1 39.0 + - - +
330C GLU* 3.1 36.1 + - - +
332C ASP* 1.3 79.1 - - - +
334C VAL* 1.3 74.8 + - + +
335C ILE 3.4 0.3 + - - -
336C GLY 4.5 0.5 + - - -
348C LYS 5.5 2.0 + - - -
350C PRO* 6.0 0.6 - - - +
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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
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194A LYS* 4.4 22.4 - - - +
330C GLU* 3.0 20.6 + - + +
333C ARG* 1.3 95.4 - - + +
335C ILE* 1.3 64.0 + - + +
339C ARG* 3.7 10.4 + - - -
345C ASP* 4.4 7.2 - - - +
348C LYS* 4.0 36.8 - - + +
349C MET* 3.9 33.0 - - + -
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Residues in contact with ILE 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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194A LYS* 6.0 2.7 - - - -
331C ILE* 3.0 16.8 + - + +
333C ARG 3.4 0.4 - - - -
334C VAL* 1.3 88.9 - - + +
336C GLY* 1.3 68.1 + - - +
338C ASN* 4.7 1.2 + - - +
339C ARG* 3.8 41.2 + - - +
341C PRO* 3.9 19.1 - - + -
345C ASP* 3.6 27.1 - - + +
349C MET* 3.8 23.6 - - + -
454C THR* 4.1 10.5 - - + -
458C GLN* 3.6 18.4 - - - +
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Residues in contact with GLY 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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331C ILE* 3.4 5.9 + - - +
332C ASP* 3.2 24.6 + - - +
333C ARG 4.5 0.4 + - - -
335C ILE* 1.3 83.9 - - - +
337C LYS* 1.3 63.9 + - - +
338C ASN 3.5 0.9 - - - -
458C GLN* 3.2 21.3 + - - +
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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