Contacts of the helix formed by residues 415 - 431 (chain C) in PDB entry 2I2X
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 SER 415 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414C LEU* 1.3 72.6 - - - +
416C ARG* 1.3 63.3 + - - +
417C PHE* 3.5 5.2 + - - +
418C GLU* 3.0 40.4 + - - +
419C THR* 2.9 27.2 + - - -
17D ASN* 4.3 12.3 + - - -
18D VAL* 4.0 18.3 - - - +
21D GLU* 3.6 19.0 + - - -
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Residues in contact with ARG 416 (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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414C LEU 4.0 0.2 + - - -
415C SER* 1.3 69.4 - - - +
417C PHE* 1.3 64.4 + - - +
419C THR* 3.1 8.8 + - - -
420C LYS* 3.0 24.0 + - - +
18D VAL 5.6 1.8 + - - -
21D GLU* 2.9 40.7 + - - +
22D LYS 2.8 31.3 + - - -
23D ALA* 3.8 17.5 + - - +
24D LEU 5.7 0.6 + - - -
25D THR* 6.1 4.0 - - - -
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Residues in contact with PHE 417 (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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179C ASN* 6.0 1.8 - - - -
239C ALA* 4.5 13.7 - - + -
415C SER* 3.2 4.7 - - - +
416C ARG* 1.3 77.0 - - - +
418C GLU* 1.3 64.4 + - + +
420C LYS* 3.3 7.5 + - + +
421C ALA* 3.0 24.8 + - + +
21D GLU* 2.9 18.8 + - - +
26D PRO* 4.1 21.1 - - + -
92D VAL 3.6 25.6 - - - -
93D ILE* 4.2 2.9 - - + -
94D PHE* 3.5 47.8 - + + -
97D ASN* 3.4 31.2 - - - -
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Residues in contact with GLU 418 (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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233C LEU 5.5 0.7 - - - +
239C ALA* 5.1 3.8 - - + -
240C HIS* 4.0 26.2 + - - +
241C THR* 2.8 43.5 + - + +
365C PRO* 5.0 1.3 - - - -
414C LEU* 3.4 11.7 - - + +
415C SER* 3.0 33.0 + - - +
417C PHE* 1.3 80.9 - - + +
419C THR* 1.3 62.3 + - - +
421C ALA* 4.7 1.1 - - - -
422C LEU* 3.1 9.9 + - - +
15D ARG* 2.9 44.4 + - - -
17D ASN* 3.7 9.3 - - - +
94D PHE* 6.1 3.8 - - + -
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Residues in contact with THR 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ALA* 5.6 3.9 - - + +
414C LEU* 3.6 22.4 + - + +
415C SER 2.9 13.9 + - - -
416C ARG* 3.1 12.0 + - - -
418C GLU* 1.3 77.4 - - - +
420C LYS* 1.3 57.2 + - - +
422C LEU* 3.4 12.5 + - + +
423C ALA* 3.0 28.9 + - + +
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Residues in contact with LYS 420 (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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416C ARG 3.0 14.4 + - - +
417C PHE* 3.3 8.3 + - + +
419C THR* 1.3 75.7 - - - +
421C ALA* 1.3 56.3 + - - +
423C ALA* 3.0 10.3 + - + +
424C ASP* 2.8 65.8 + - - +
27D GLU* 4.8 15.7 + - - +
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Residues in contact with ALA 421 (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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179C ASN* 6.0 1.6 - - - +
239C ALA* 3.7 27.6 - - + -
241C THR* 3.8 5.4 - - - +
242C ILE* 4.0 18.6 - - + +
417C PHE* 3.0 23.0 + - + +
420C LYS* 1.3 76.7 - - - +
422C LEU* 1.3 62.5 + - - +
424C ASP* 3.5 9.4 + - - +
425C ALA* 3.0 25.5 + - - +
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Residues in contact with LEU 422 (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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241C THR* 3.8 24.1 + - - +
245C ILE* 4.5 3.1 - - + -
401C CYS* 4.1 30.3 - - - +
404C ILE* 3.9 32.3 - - + -
405C GLU* 3.6 36.1 - - + +
408C ALA* 6.0 0.7 - - + -
414C LEU* 4.8 8.1 - - + -
418C GLU 3.1 18.8 + - - +
419C THR* 3.5 9.2 - - + +
420C LYS 3.1 0.2 - - - -
421C ALA* 1.3 77.4 - - - +
423C ALA* 1.3 56.5 + - - +
425C ALA* 3.4 4.0 + - - +
426C LYS* 3.0 27.9 + - - +
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Residues in contact with ALA 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C GLU* 4.8 8.7 - - - +
419C THR* 3.0 16.3 + - + +
420C LYS* 3.0 13.0 + - + +
422C LEU* 1.3 72.9 - - - +
424C ASP* 1.3 69.2 + - - +
426C LYS* 3.5 5.5 + - - +
427C ALA* 3.1 24.9 + - - +
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Residues in contact with ASP 424 (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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420C LYS* 2.8 55.4 + - - +
421C ALA* 3.7 7.8 - - - +
423C ALA* 1.3 74.6 - - - +
425C ALA* 1.3 56.7 + - - +
427C ALA* 3.4 5.4 + - - +
428C ALA* 2.9 27.2 + - - +
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Residues in contact with ALA 425 (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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181C ILE* 3.5 34.3 - - + +
242C ILE* 5.1 2.2 - - + -
245C ILE* 3.7 26.2 - - + -
421C ALA 3.0 18.1 + - - +
422C LEU 3.9 2.0 - - - +
424C ASP* 1.3 74.3 - - - +
426C LYS* 1.3 61.4 + - - +
428C ALA* 3.1 3.2 + - - +
429C LEU* 2.8 35.3 + - - +
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Residues in contact with LYS 426 (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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398C ILE* 4.5 6.5 - - + +
401C CYS* 3.9 27.4 - - + -
402C ASN* 2.8 27.9 + - - +
405C GLU* 3.3 34.5 + - - +
422C LEU 3.0 16.8 + - - +
423C ALA* 3.9 4.0 - - - +
424C ASP 3.4 0.2 - - - -
425C ALA* 1.3 76.0 - - - +
427C ALA* 1.3 57.7 + - - +
429C LEU* 3.2 6.2 + - - +
430C GLU* 2.8 66.1 + - + +
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Residues in contact with ALA 427 (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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423C ALA 3.1 18.3 + - - +
424C ASP* 3.7 6.3 - - - +
426C LYS* 1.3 78.3 - - - +
428C ALA* 1.3 60.6 + - - +
430C GLU* 3.4 8.0 + - - +
431C ALA* 3.1 25.1 + - - +
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Residues in contact with ALA 428 (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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181C ILE* 4.4 16.2 - - + -
182C PRO* 4.4 13.2 - - + +
424C ASP 2.9 15.0 + - - +
425C ALA* 3.1 11.2 + - - +
427C ALA* 1.3 76.8 - - - +
429C LEU* 1.3 63.4 + - - +
431C ALA* 3.4 11.9 + - - +
432C LEU* 3.5 19.0 + - - +
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Residues in contact with LEU 429 (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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181C ILE* 3.8 26.7 - - + +
182C PRO* 6.3 0.2 - - + -
185C LEU* 4.2 26.9 - - + -
245C ILE* 4.4 4.5 - - + -
249C ILE* 5.3 0.7 - - + -
394C LYS* 4.0 16.6 + - + +
397C ALA* 3.8 45.8 - - + +
398C ILE* 3.7 16.9 - - + +
401C CYS* 4.0 14.4 - - - -
425C ALA* 2.8 21.2 + - + +
426C LYS* 3.6 3.4 - - - +
428C ALA* 1.3 79.2 - - - +
430C GLU* 1.3 60.6 + - - +
432C LEU* 3.3 24.3 + - + +
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Residues in contact with GLU 430 (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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394C LYS* 6.1 0.2 - - - +
398C ILE* 3.9 25.0 - - + +
426C LYS* 2.8 69.3 + - + +
427C ALA* 4.1 7.2 + - - +
429C LEU* 1.3 74.0 - - - +
431C ALA* 1.3 60.2 + - - +
432C LEU 3.3 5.5 + - - +
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Residues in contact with ALA 431 (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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427C ALA 3.1 16.3 + - - +
428C ALA* 3.8 7.4 - - - +
429C LEU 3.3 0.4 - - - -
430C GLU* 1.3 77.1 - - - +
432C LEU* 1.3 63.3 + - + +
433C PRO* 3.9 2.1 - - - +
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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