Contacts of the helix formed by residues 384 - 396 (chain C) in PDB entry 4X4S
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 THR 384 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313C PHE* 3.5 10.8 - - - -
336C LYS 3.6 12.8 - - - +
337C GLU* 4.3 12.6 - - + +
382C PHE* 3.7 0.4 - - - -
383C THR* 1.3 94.4 + - - +
385C PRO* 1.3 75.6 - - - +
386C GLU* 3.6 10.7 + - - +
387C GLU* 3.2 29.3 + - + +
388C GLY 2.9 18.2 + - - -
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Residues in contact with PRO 385 (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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277C ALA* 4.2 8.3 - - + -
279C PHE* 3.5 25.4 - - + -
308C LEU* 4.1 9.1 - - + +
313C PHE* 3.5 27.8 - - + -
333C CYS* 4.2 5.2 - - + -
335C ILE 3.0 23.1 - - - +
336C LYS 3.3 19.5 - - - +
384C THR* 1.3 81.5 - - - +
386C GLU* 1.3 72.4 + - - +
388C GLY* 3.1 1.2 + - - -
389C VAL* 2.9 29.5 + - - +
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Residues in contact with GLU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ALA* 4.3 12.7 - - - +
278C VAL 5.1 0.7 + - - +
279C PHE* 3.7 38.8 - - + +
336C LYS 4.4 2.3 - - - +
384C THR* 3.6 10.5 - - - +
385C PRO* 1.3 89.8 - - - +
387C GLU* 1.3 68.7 + - + +
389C VAL* 3.6 0.9 + - - +
390C ARG* 3.2 23.5 + - - +
414C ILE* 3.9 25.7 - - + +
416C SER* 3.6 22.3 + - - -
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Residues in contact with GLU 387 (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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382C PHE* 3.9 19.3 - - + +
383C THR* 5.4 1.6 - - - +
384C THR* 3.2 23.3 + - + +
386C GLU* 1.3 83.4 - - + +
388C GLY* 1.3 62.7 + - - +
390C ARG* 2.6 43.1 + - - +
391C SER* 3.2 21.8 + - - -
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Residues in contact with GLY 388 (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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307C PHE* 3.0 27.2 - - - -
313C PHE* 4.8 2.2 - - - -
382C PHE* 3.7 25.7 - - - +
384C THR 2.9 15.4 + - - -
385C PRO 3.1 3.1 + - - -
387C GLU* 1.3 74.5 - - - +
389C VAL* 1.3 62.8 + - - +
391C SER* 3.3 4.2 + - - -
392C TYR 3.0 13.7 + - - -
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Residues in contact with VAL 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C PHE* 3.6 18.2 - - + -
281C VAL* 3.7 26.2 - - + -
304C ILE* 3.5 34.5 - - + -
307C PHE* 3.8 7.4 - - + -
308C LEU* 3.6 26.0 - - + -
385C PRO 2.9 19.8 + - - +
386C GLU 4.1 2.7 - - - +
388C GLY* 1.3 73.2 - - - +
390C ARG* 1.3 56.4 + - - +
392C TYR* 3.1 1.8 + - - +
393C ALA* 2.7 36.6 + - + +
414C ILE* 4.4 4.0 - - + -
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Residues in contact with ARG 390 (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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386C GLU* 3.2 15.8 + - - +
387C GLU* 2.6 44.1 + - - +
389C VAL* 1.3 79.5 - - - +
391C SER* 1.3 63.1 + - - +
394C SER* 3.0 32.7 + - - +
412C PHE* 3.6 26.4 - - + -
413C GLU* 6.0 0.8 - - - +
414C ILE* 3.9 37.5 + - + +
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Residues in contact with SER 391 (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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307C PHE* 5.7 0.4 - - - -
381C LYS* 6.1 1.4 - - - +
382C PHE* 4.2 22.5 - - - -
387C GLU 3.2 14.4 + - - -
388C GLY 3.6 8.5 - - - -
389C VAL 3.3 0.2 - - - -
390C ARG* 1.3 76.0 - - - +
392C TYR* 1.3 64.2 + - - +
394C SER* 3.2 6.6 + - - -
395C THR* 3.1 32.6 + - - +
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Residues in contact with TYR 392 (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 LYS* 3.6 31.4 + - - +
304C ILE* 4.1 17.0 - - + -
307C PHE* 3.4 36.7 - + + -
310C ARG* 3.5 21.1 + - - -
388C GLY 3.0 13.1 + - - +
389C VAL 3.5 6.7 - - - +
391C SER* 1.3 77.4 - - - +
393C ALA* 1.3 58.1 + - - +
395C THR* 3.9 4.0 - - - -
396C HIS* 2.7 64.7 + + + +
399C THR* 3.7 3.8 - - - +
400C LEU* 3.8 22.2 - - + -
22D U 2.7 23.3 + - - -
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Residues in contact with ALA 393 (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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281C VAL* 5.2 4.7 - - + -
304C ILE* 5.3 3.6 - - + -
389C VAL* 2.7 27.3 + - + +
392C TYR* 1.3 79.5 - - + +
394C SER* 1.3 60.6 + - - +
397C TRP* 3.3 23.8 - - - +
400C LEU* 4.4 11.9 - - + -
408C ILE* 3.7 18.5 - - + +
409C ARG* 5.5 0.3 - - - -
412C PHE* 3.6 27.3 - - + -
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Residues in contact with SER 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C ARG* 3.0 25.6 + - - +
391C SER* 3.5 6.7 - - - -
393C ALA* 1.3 77.8 - - - +
395C THR* 1.3 61.5 + - - +
397C TRP* 3.2 22.7 - - - -
412C PHE* 3.8 14.6 - - - -
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Residues in contact with THR 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C SER* 3.1 22.4 + - - +
392C TYR* 3.3 3.5 + - - -
394C SER* 1.3 82.8 - - - +
396C HIS* 1.3 86.8 + - - +
397C TRP* 3.3 13.7 + - - -
398C HIS* 4.9 1.0 + - - +
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Residues in contact with HIS 396 (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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310C ARG* 6.0 0.4 - - - -
392C TYR* 2.7 54.6 + + + +
393C ALA 4.2 0.2 - - - -
395C THR* 1.3 99.8 + - - +
397C TRP* 1.3 63.3 + - - +
398C HIS* 3.1 4.5 + - - +
399C THR* 3.4 12.3 - - + +
400C LEU* 3.3 17.7 - - - +
21D C 3.1 21.1 + - - +
22D U 3.6 35.4 + - - -
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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