Contacts of the helix formed by residues 351 - 365 (chain C) in PDB entry 2XH2
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 351 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C ASP* 3.5 34.1 - - + +
93C LEU* 5.2 0.2 - - + -
94C ILE* 4.2 8.9 - - + +
102C LYS* 4.0 4.9 - - - -
110C ILE* 3.7 17.9 - - + -
111C LEU* 4.2 5.8 - - - -
114C SER* 3.7 4.5 - - - +
346C VAL* 5.6 0.2 - - - -
349C ILE* 3.6 4.1 + - - +
350C GLY* 1.3 83.6 - - - +
352C LEU* 1.3 62.3 + - - +
353C SER 3.8 0.3 + - - -
354C GLU* 2.8 41.0 + - - +
355C SER* 3.0 25.6 + - - -
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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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86C GLN* 3.7 18.4 - - + +
111C LEU* 4.5 2.6 - - - +
114C SER* 3.0 19.6 + - - +
115C LEU* 4.4 10.5 - - + -
118C SER* 3.5 35.4 - - - +
133C LEU* 3.8 13.9 - - + -
136C LEU* 4.0 3.8 - - + -
346C VAL* 5.0 3.1 - - + -
351C THR* 1.3 69.8 - - - +
353C SER* 1.3 60.4 + - - +
355C SER* 3.1 10.7 + - - -
356C ILE* 2.9 46.3 + - + +
382C PHE* 3.8 25.6 - - + -
386C LEU* 4.0 13.7 - - + -
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Residues in contact with SER 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLN* 3.2 26.6 + - - +
87C LYS* 3.5 17.1 + - - +
90C ASP* 2.7 34.7 + - - -
351C THR* 3.4 0.6 - - - -
352C LEU* 1.3 76.3 - - - +
354C GLU* 1.3 60.5 + - - +
356C ILE* 3.4 9.3 + - - +
357C LYS* 3.0 27.4 + - - +
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Residues in contact with GLU 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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94C ILE* 3.7 19.7 - - + +
102C LYS* 2.9 34.5 + - - -
327C PRO* 4.1 11.1 - - + +
349C ILE* 3.7 32.2 - - + +
351C THR* 2.8 24.6 + - - +
353C SER* 1.3 77.2 - - - +
355C SER* 1.3 57.8 - - - +
357C LYS* 3.3 8.4 + - - +
358C ALA* 2.9 28.8 + - - +
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Residues in contact with SER 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C THR* 4.2 2.5 - - - +
344C LEU* 3.6 21.0 - - - +
346C VAL* 3.4 34.8 - - - +
349C ILE* 3.4 17.9 - - - +
351C THR 3.0 17.2 + - - -
352C LEU* 3.1 12.1 + - - -
354C GLU* 1.3 77.8 - - - +
356C ILE* 1.3 61.1 + - - +
358C ALA* 3.3 8.1 + - - +
359C ALA 3.0 17.7 + - - -
386C LEU* 5.6 1.3 - - - -
390C LEU* 5.9 0.4 - - - -
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Residues in contact with ILE 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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86C GLN* 5.5 0.9 - - + -
133C LEU* 4.9 4.7 - - + +
136C LEU* 3.9 34.8 - - + +
137C SER* 3.8 17.0 - - - -
352C LEU* 2.9 45.2 + - + +
353C SER* 3.8 7.2 - - - +
355C SER* 1.3 73.7 - - - +
357C LYS* 1.3 59.5 + - - +
359C ALA* 3.2 7.3 + - - +
360C GLN* 2.9 54.0 + - + +
386C LEU* 4.9 4.7 - - + -
390C LEU* 4.4 13.9 - - + -
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Residues in contact with LYS 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C PRO* 4.1 14.7 - - + +
353C SER 3.0 14.9 + - - +
354C GLU* 3.5 12.1 - - - +
355C SER 3.3 0.2 - - - -
356C ILE* 1.3 75.8 - - - +
358C ALA* 1.3 58.7 + - - +
360C GLN* 3.2 15.7 + - + +
361C ASP* 2.8 70.7 + - - +
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Residues in contact with ALA 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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325C THR* 3.8 20.2 - - + +
327C PRO* 4.1 8.7 - - + +
330C ILE* 3.5 26.1 - - + +
342C LEU* 3.8 10.5 - - + +
354C GLU 2.9 15.2 + - - +
355C SER 3.5 8.3 - - - +
356C ILE 3.2 0.2 - - - -
357C LYS* 1.3 78.1 - - - +
359C ALA* 1.3 56.4 + - - +
361C ASP* 3.6 4.0 + - - +
362C SER* 2.7 34.3 + - - -
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Residues in contact with ALA 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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342C LEU* 4.2 1.2 - - - +
344C LEU* 3.8 23.1 - - + -
355C SER 3.0 8.1 + - - +
356C ILE 3.5 7.4 - - - +
358C ALA* 1.3 77.3 - - - +
360C GLN* 1.3 57.7 + - + +
362C SER* 3.2 3.5 + - - -
363C PHE* 2.9 40.5 + - + -
369C VAL* 4.0 16.8 - - + +
390C LEU* 4.0 22.7 - - + -
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Residues in contact with GLN 360 (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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87C LYS* 6.2 0.2 - - - -
136C LEU 4.4 2.4 + - - -
137C SER* 3.0 42.2 + - - +
138C LYS* 4.8 5.7 - - - +
356C ILE* 2.9 30.8 + - + +
357C LYS* 3.7 18.5 - - + +
359C ALA* 1.3 75.1 - - + +
361C ASP* 1.3 67.9 + - - +
363C PHE* 3.4 10.9 + - + +
364C ALA* 3.0 25.8 + - - +
390C LEU* 5.9 0.9 - - + -
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Residues in contact with ASP 361 (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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327C PRO* 3.5 23.4 - - - +
330C ILE* 4.4 13.0 - - + -
334C ILE* 4.0 8.9 - - + +
357C LYS* 2.8 59.6 + - - +
358C ALA* 3.8 4.9 - - - +
360C GLN* 1.3 73.2 - - - +
362C SER* 1.3 64.2 + - - +
364C ALA* 3.4 6.4 + - - +
365C ALA* 3.2 21.8 + - - +
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Residues in contact with SER 362 (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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330C ILE* 4.0 13.6 - - - +
342C LEU* 3.5 19.2 - - - +
358C ALA 2.7 23.2 + - - -
359C ALA 3.4 5.2 - - - -
360C GLN 3.2 0.2 - - - -
361C ASP* 1.3 76.3 - - - +
363C PHE* 1.3 63.1 + - - +
365C ALA* 3.0 9.7 + - - +
367C TRP* 2.9 46.0 + - - +
369C VAL* 3.8 17.7 - - - -
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Residues in contact with PHE 363 (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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139C SER* 5.9 0.4 - - - -
359C ALA* 2.9 32.8 + - + +
360C GLN* 3.9 9.0 - - + +
362C SER* 1.3 76.6 - - - +
364C ALA* 1.3 57.8 + - - +
366C GLY 3.1 11.8 + - - -
367C TRP 3.5 13.0 - - - -
368C GLY* 4.4 0.7 - - - -
369C VAL* 3.6 37.7 - - + -
390C LEU* 3.5 26.0 - - + -
392C THR* 3.9 15.5 - - + -
431C HIS 5.5 0.2 - - - -
434C ASP* 3.2 48.5 - - + +
435C LYS* 3.1 23.1 + - - +
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Residues in contact with ALA 364 (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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360C GLN 3.0 18.4 + - - +
361C ASP* 3.7 7.6 - - - +
362C SER 3.2 0.4 - - - -
363C PHE* 1.3 77.1 - - - +
365C ALA* 1.3 58.9 + - - +
366C GLY 3.2 1.0 + - - -
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Residues in contact with ALA 365 (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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334C ILE* 3.5 47.3 - - + -
361C ASP 3.2 3.9 + - - +
362C SER 3.0 9.0 + - - +
364C ALA* 1.3 75.4 - - - +
366C GLY* 1.3 61.5 + - - +
367C TRP* 3.3 12.5 + - + +
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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