Contacts of the helix formed by residues 345 - 359 (chain C) in PDB entry 2XSD
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 345 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343C SER 3.9 9.6 - - - +
344C ILE* 1.3 80.7 - - - +
346C VAL* 1.3 54.2 + - - +
347C GLY 3.2 3.6 - - - +
348C VAL* 2.7 39.2 + - + +
349C LYS* 2.7 18.3 + - - -
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Residues in contact with VAL 346 (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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344C ILE 4.3 0.2 + - - -
345C GLU* 1.3 72.6 - - - +
347C GLY* 1.3 63.9 + - - +
349C LYS* 4.2 15.9 - - + +
350C GLY* 3.1 22.0 + - - +
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Residues in contact with GLY 347 (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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345C GLU* 3.0 3.4 + - - +
346C VAL* 1.3 80.5 - - - +
348C VAL* 1.3 64.3 + - - +
350C GLY* 4.3 0.5 - - - -
351C ALA* 3.5 18.2 + - - +
374C LEU* 5.3 1.5 - - - +
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Residues in contact with VAL 348 (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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344C ILE* 3.3 21.1 - - + -
345C GLU* 2.7 27.8 + - + +
347C GLY* 1.3 72.1 - - - -
349C LYS* 1.3 62.4 + - - +
351C ALA* 3.1 6.2 + - - +
352C LEU* 2.9 23.4 + - + +
374C LEU* 3.3 47.3 - - + +
376C LEU* 3.3 24.0 - - + -
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Residues in contact with LYS 349 (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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203A G 4.3 25.8 + - - -
204A C 3.9 23.3 - - - +
343C SER* 5.3 1.0 + - - -
344C ILE* 3.4 37.5 + - + +
345C GLU 2.7 18.6 + - - +
346C VAL* 3.9 14.0 - - + +
348C VAL* 1.3 72.8 - - - +
350C GLY* 1.3 62.9 + - - +
352C LEU* 3.1 9.5 + - - +
353C GLU* 2.9 23.5 + - - +
384C TRP* 4.5 10.9 - - + +
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Residues in contact with GLY 350 (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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346C VAL* 3.1 13.9 + - - +
347C GLY 4.3 0.7 - - - -
349C LYS* 1.3 77.4 - - - +
351C ALA* 1.3 62.8 + - - +
353C GLU* 3.2 9.6 + - - +
354C SER* 3.0 24.8 + - - -
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Residues in contact with ALA 351 (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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347C GLY 3.5 12.5 + - - +
348C VAL* 3.1 10.8 + - - +
350C GLY* 1.3 72.2 - - - +
352C LEU* 1.3 66.8 + - - +
354C SER* 2.9 20.3 + - - -
355C HIS* 3.2 26.3 + - + +
374C LEU* 4.5 15.5 - - + -
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Residues in contact with LEU 352 (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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344C ILE* 4.0 16.8 - - + -
348C VAL* 2.9 33.3 + - + +
349C LYS* 3.4 7.6 - - - +
351C ALA* 1.3 75.2 - - - +
353C GLU* 1.3 63.4 + - - +
355C HIS* 3.4 7.4 + - - +
356C PHE* 3.1 21.3 + - - +
370C LEU* 3.5 32.3 - - + -
374C LEU* 3.7 8.5 - - + -
376C LEU* 4.4 3.4 - - + -
381C VAL* 4.5 9.2 - - + -
384C TRP* 3.6 44.7 - - + +
385C PHE* 4.0 16.4 - - + -
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Residues in contact with GLU 353 (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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349C LYS 2.9 12.8 + - - +
350C GLY* 3.3 12.6 - - - +
351C ALA 3.1 0.2 - - - -
352C LEU* 1.3 75.3 - - - +
354C SER* 1.3 66.8 + - - +
356C PHE* 3.1 14.2 + - - +
357C LEU* 3.2 43.3 + - + +
384C TRP* 3.6 10.1 - - + -
388C ARG* 2.9 46.9 + - - +
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Residues in contact with SER 354 (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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350C GLY 3.0 14.7 + - - -
351C ALA* 2.9 12.5 + - - -
353C GLU* 1.3 76.1 - - - +
355C HIS* 1.3 66.9 + - - +
357C LEU* 3.2 24.6 + - - +
358C LYS* 3.4 21.2 + - - +
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Residues in contact with HIS 355 (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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351C ALA* 3.2 28.1 + - + +
352C LEU 3.8 5.4 - - - +
354C SER* 1.3 80.3 - - - +
356C PHE* 1.3 53.3 + - - +
358C LYS* 2.8 23.6 + - - +
359C CYS* 2.6 46.7 + - - +
370C LEU* 3.4 36.7 - - + +
374C LEU* 6.1 0.4 - - + -
385C PHE* 4.3 5.6 - - + -
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Residues in contact with PHE 356 (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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352C LEU 3.1 13.4 + - - +
353C GLU* 3.1 15.9 + - - +
355C HIS* 1.3 77.7 - - - +
357C LEU* 1.3 68.0 + - + +
358C LYS 3.2 0.5 + - - -
359C CYS 4.0 0.9 - - - -
360C PRO* 3.3 57.3 - - + +
384C TRP* 4.3 4.3 - - + -
385C PHE* 3.8 24.0 - + + -
388C ARG* 3.2 61.9 - - + -
389C ARG* 4.0 15.5 - - + -
392C GLU* 3.7 21.3 - - + -
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Residues in contact with LEU 357 (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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353C GLU* 3.2 39.4 + - + +
354C SER* 3.2 13.9 + - - +
356C PHE* 1.3 84.7 - - + +
358C LYS* 1.3 63.3 + - + +
360C PRO* 4.7 3.9 - - - +
388C ARG* 4.9 2.5 - - - +
392C GLU* 5.8 0.9 - - - +
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Residues in contact with LYS 358 (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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354C SER* 3.7 19.5 - - - +
355C HIS* 2.8 22.4 + - - +
357C LEU* 1.3 81.2 - - + +
359C CYS* 1.3 62.3 + - + +
360C PRO* 3.2 10.0 - - - +
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Residues in contact with CYS 359 (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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355C HIS* 2.6 31.9 + - - +
356C PHE 3.7 2.7 - - - -
358C LYS* 1.3 76.8 - - + +
360C PRO* 1.3 65.4 - - - +
361C LYS 3.2 8.9 + - - +
362C PRO* 3.9 19.9 - - + +
366C GLU* 5.4 10.8 - - + +
370C LEU* 6.4 0.4 - - - -
385C PHE* 3.7 13.0 - - - -
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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