Contacts of the helix formed by residues 415 - 431 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414E LEU* 1.3 73.2 - - - +
416E ARG* 1.3 60.5 + - - +
417E PHE* 3.5 5.4 + - - +
418E GLU* 3.0 35.9 + - - +
419E THR* 2.9 30.0 + - - -
17F ASN* 4.3 13.5 + - - -
18F VAL* 3.8 20.9 - - - +
21F GLU* 3.5 19.7 + - - -
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Residues in contact with ARG 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414E LEU 4.0 0.8 + - - +
415E SER* 1.3 70.5 - - - +
417E PHE* 1.3 57.2 + - - +
419E THR* 3.4 8.6 + - - -
420E LYS* 2.9 31.2 + - - +
18F VAL 5.4 2.8 + - - -
21F GLU* 2.9 41.6 + - - +
22F LYS 3.1 28.5 + - - -
23F ALA* 4.1 14.4 + - - +
24F LEU 5.6 0.8 + - - -
25F THR* 6.1 6.1 - - - +
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Residues in contact with PHE 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ASN* 6.1 1.8 - - - -
239E ALA* 4.7 12.8 - - + -
415E SER* 3.9 3.8 - - - +
416E ARG* 1.3 76.9 - - - +
418E GLU* 1.3 61.7 + - + +
420E LYS* 3.6 6.2 + - + +
421E ALA* 3.2 23.6 + - + +
21F GLU* 2.9 19.6 + - - +
26F PRO* 4.3 18.8 - - + -
92F VAL 3.9 23.3 - - - -
93F ILE* 4.2 3.8 - - + -
94F PHE* 3.4 47.6 - + + -
97F ASN* 3.3 32.3 - - - -
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Residues in contact with GLU 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E ALA* 5.2 4.0 - - + -
240E HIS* 3.8 23.8 - - - +
241E THR* 2.7 48.0 + - + +
365E PRO* 5.0 0.7 - - - -
414E LEU* 3.5 11.0 - - + +
415E SER* 3.0 35.6 + - - +
417E PHE* 1.3 76.3 - - + +
419E THR* 1.3 67.6 + - - +
421E ALA* 3.4 0.4 + - - -
422E LEU* 3.1 12.8 + - - +
15F ARG* 3.0 36.3 + - - -
17F ASN* 3.7 8.8 - - - +
94F PHE* 6.1 3.6 - - + -
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Residues in contact with THR 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414E LEU* 3.5 26.9 + - + +
415E SER 2.9 17.5 + - - -
416E ARG* 3.6 9.0 - - - -
418E GLU* 1.3 78.4 - - - +
420E LYS* 1.3 61.6 + - - +
422E LEU* 3.3 9.2 + - + +
423E ALA* 3.2 20.3 + - + +
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Residues in contact with LYS 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416E ARG 2.9 18.4 + - - +
417E PHE* 3.8 7.9 - - + +
418E GLU 3.3 0.2 - - - -
419E THR* 1.3 76.8 - - - +
421E ALA* 1.3 57.5 + - - +
423E ALA* 3.2 9.9 + - + +
424E ASP* 3.0 58.6 + - - +
27F GLU* 5.3 11.3 + - - +
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Residues in contact with ALA 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ASN* 5.8 2.2 - - - +
239E ALA* 3.8 26.0 - - + -
241E THR* 3.9 5.6 - - - +
242E ILE* 4.2 17.8 - - + +
417E PHE* 3.2 23.4 + - + +
420E LYS* 1.3 73.2 - - - +
422E LEU* 1.3 60.2 + - - +
424E ASP* 3.9 9.3 - - - +
425E ALA* 3.0 29.3 + - - +
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Residues in contact with LEU 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E THR* 4.0 27.1 + - + +
245E ILE* 4.3 3.8 - - + -
401E CYS* 3.8 33.2 - - - +
404E ILE* 4.0 31.6 - - + -
405E GLU* 4.1 32.3 - - + +
414E LEU* 4.8 8.5 - - + -
418E GLU 3.1 13.7 + - - +
419E THR* 3.4 13.2 - - + +
421E ALA* 1.3 78.5 - - - +
423E ALA* 1.3 50.1 + - - +
425E ALA* 3.4 4.8 + - - +
426E LYS* 2.8 32.9 + - - +
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Residues in contact with ALA 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E GLU* 5.3 5.4 - - - +
419E THR* 3.2 9.4 + - + +
420E LYS* 3.2 13.9 + - + +
422E LEU* 1.3 77.3 - - - +
424E ASP* 1.3 66.5 + - - +
426E LYS* 3.8 6.8 - - - +
427E ALA* 3.1 26.0 + - - +
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Residues in contact with ASP 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E ILE* 5.4 0.7 - - - -
420E LYS* 3.0 47.0 + - - +
421E ALA* 4.0 7.8 - - - +
423E ALA* 1.3 77.9 - - - +
425E ALA* 1.3 64.4 + - - +
427E ALA* 4.0 4.3 - - - +
428E ALA* 3.1 25.7 + - - +
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Residues in contact with ALA 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E ILE* 3.8 33.1 - - + +
242E ILE* 5.2 1.8 - - + -
245E ILE* 3.5 30.3 - - + -
421E ALA 3.0 18.6 + - - +
422E LEU 3.6 2.0 - - - +
424E ASP* 1.3 77.8 - - - +
426E LYS* 1.3 61.6 + - - +
428E ALA* 3.5 1.8 + - - +
429E LEU* 3.0 30.1 + - - +
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Residues in contact with LYS 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398E ILE* 6.1 4.5 - - + -
401E CYS* 4.0 23.5 - - + -
402E ASN* 2.9 36.8 + - - +
405E GLU* 3.0 37.4 + - - +
422E LEU 2.8 21.2 + - - +
423E ALA* 3.8 7.6 - - - +
424E ASP 3.3 0.4 - - - -
425E ALA* 1.3 72.0 - - - +
427E ALA* 1.3 62.7 + - - +
429E LEU* 2.9 16.9 + - - +
430E GLU* 3.0 45.0 + - + +
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Residues in contact with ALA 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E ALA 3.1 15.3 + - - +
424E ASP* 4.0 4.7 - - - +
426E LYS* 1.3 77.6 - - - +
428E ALA* 1.3 56.9 + - - +
430E GLU* 3.3 8.0 + - - +
431E ALA* 3.1 32.3 + - - +
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Residues in contact with ALA 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E ILE* 4.8 5.2 - - + -
182E PRO* 4.6 20.1 - - + +
424E ASP 3.1 18.8 + - - +
425E ALA* 3.8 6.7 - - - +
427E ALA* 1.3 76.2 - - - +
429E LEU* 1.3 59.0 + - - +
431E ALA* 4.1 6.2 + - - +
432E LEU* 3.3 27.0 + - - +
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Residues in contact with LEU 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E ILE* 3.8 25.1 - - + -
185E LEU* 4.2 28.3 - - + -
245E ILE* 4.5 4.7 - - + -
249E ILE* 5.5 0.4 - - + -
394E LYS* 4.0 18.4 + - + +
397E ALA* 3.8 44.6 - - + +
398E ILE* 4.0 15.9 - - + +
401E CYS* 4.5 9.2 - - - -
425E ALA 3.0 20.0 + - - +
426E LYS* 2.9 8.0 + - - +
428E ALA* 1.3 76.3 - - - +
430E GLU* 1.3 63.5 + - - +
431E ALA 3.3 0.7 - - - -
432E LEU* 3.4 23.8 + - + +
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Residues in contact with GLU 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394E LYS* 5.6 1.4 + - - +
398E ILE* 4.4 23.8 - - + -
426E LYS* 3.0 53.9 + - + +
427E ALA* 3.3 6.8 + - - +
429E LEU* 1.3 73.4 - - - +
431E ALA* 1.3 59.9 + - - +
432E LEU 3.2 11.9 + - - +
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Residues in contact with ALA 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E ALA 3.1 16.8 + - - +
428E ALA* 4.5 6.5 - - - +
429E LEU 3.3 0.4 - - - -
430E GLU* 1.3 75.5 - - - +
432E LEU* 1.3 63.4 + - - +
433E PRO* 3.9 3.1 - - - +
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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