Contacts of the helix formed by residues 415 - 431 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414G LEU* 1.3 72.1 - - - +
416G ARG* 1.3 61.4 + - - +
417G PHE* 3.6 4.3 + - - +
418G GLU* 2.9 42.8 + - - +
419G THR* 2.9 28.0 + - - -
17H ASN* 4.3 11.4 + - - -
18H VAL* 3.9 18.6 - - - +
21H GLU* 3.7 19.4 + - - -
94H PHE* 6.1 0.2 - - - -
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Residues in contact with ARG 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G SER* 1.3 68.7 - - - +
417G PHE* 1.3 66.3 + - - +
419G THR* 3.1 7.4 + - - -
420G LYS* 2.9 25.1 + - - +
18H VAL 5.4 2.0 + - - -
21H GLU* 2.9 40.6 + - - +
22H LYS 3.3 26.9 + - - -
23H ALA* 4.1 15.8 + - - +
24H LEU 5.3 1.2 + - - -
25H THR* 5.3 12.3 - - + +
8K SER* 5.9 4.4 + - - -
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Residues in contact with PHE 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G ASN* 6.1 3.1 - - - -
239G ALA* 4.5 11.9 - - + -
415G SER* 3.3 4.2 - - - +
416G ARG* 1.3 72.8 - - - +
418G GLU* 1.3 59.0 + - - +
420G LYS* 3.6 6.7 - - + +
421G ALA* 2.9 37.4 + - + +
21H GLU* 2.7 20.3 + - + +
26H PRO* 4.2 21.5 - - + -
92H VAL 3.4 26.7 - - - -
93H ILE* 4.0 3.6 - - + -
94H PHE* 3.5 48.5 - + + -
97H ASN* 3.1 33.0 - - - -
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Residues in contact with GLU 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239G ALA* 5.0 3.6 - - + -
240G HIS* 4.2 23.9 + - - +
241G THR* 2.8 40.2 + - + +
365G PRO* 5.2 0.2 - - - -
414G LEU* 3.3 13.3 - - + +
415G SER* 2.9 44.3 + - - +
417G PHE* 1.3 78.6 - - + +
419G THR* 1.3 60.3 + - - +
421G ALA* 4.5 1.8 - - - -
422G LEU* 3.2 15.8 + - - +
15H ARG* 3.1 34.5 + - - -
17H ASN* 3.5 10.2 - - - +
94H PHE* 5.8 4.9 - - + -
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Residues in contact with THR 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408G ALA* 5.5 1.0 - - - +
414G LEU* 3.7 22.8 + - + +
415G SER 2.9 21.6 + - - -
416G ARG* 3.1 7.6 + - - -
418G GLU* 1.3 73.1 - - - +
420G LYS* 1.3 67.5 + - - +
422G LEU* 3.1 12.7 + - + +
423G ALA* 3.0 21.7 + - + +
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Residues in contact with LYS 420 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416G ARG 2.9 16.3 + - - +
417G PHE* 3.6 7.6 - - + +
419G THR* 1.3 76.0 - - - +
421G ALA* 1.3 56.6 + - - +
423G ALA* 2.8 30.4 + - + +
424G ASP* 3.0 40.3 + - - +
26H PRO* 6.3 3.8 - - + -
27H GLU* 3.9 26.5 - - - +
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Residues in contact with ALA 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G ASN* 5.6 2.2 - - - +
239G ALA* 3.9 26.0 - - + -
241G THR* 4.1 2.5 - - - +
242G ILE* 4.1 19.9 - - + +
417G PHE* 2.9 28.1 + - + +
418G GLU 3.9 4.3 - - - +
420G LYS* 1.3 73.1 - - - +
422G LEU* 1.3 58.5 + - - +
424G ASP* 3.8 11.9 + - - +
425G ALA* 3.4 21.0 + - - +
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Residues in contact with LEU 422 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G THR* 4.2 16.6 + - + +
245G ILE* 4.2 12.8 - - + -
401G CYS* 4.0 30.3 - - + -
404G ILE* 3.6 33.4 - - + -
405G GLU* 4.1 27.6 - - + +
408G ALA* 5.8 0.7 - - + -
414G LEU* 4.8 7.0 - - + -
418G GLU 3.2 12.8 + - - +
419G THR* 3.1 13.9 + - + +
420G LYS 3.0 0.4 - - - -
421G ALA* 1.3 76.0 - - - +
423G ALA* 1.3 65.4 + - - +
424G ASP 3.2 0.2 - - - -
425G ALA* 3.3 3.8 + - - +
426G LYS* 3.1 22.2 + - + +
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Residues in contact with ALA 423 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405G GLU* 5.3 6.3 - - - +
419G THR* 3.0 12.3 + - + +
420G LYS* 2.8 19.0 + - - +
422G LEU* 1.3 72.7 - - - +
424G ASP* 1.3 58.8 + - - +
426G LYS* 3.4 6.1 + - - +
427G ALA* 3.0 31.8 + - - +
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Residues in contact with ASP 424 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G ILE* 5.5 0.4 - - - -
420G LYS* 3.0 42.4 + - - +
421G ALA* 3.8 11.8 - - - +
422G LEU 3.2 0.2 - - - -
423G ALA* 1.3 78.1 - - - +
425G ALA* 1.3 57.7 + - - +
427G ALA* 3.8 5.1 - - - +
428G ALA* 2.9 31.8 + - - +
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Residues in contact with ALA 425 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G ILE* 3.7 31.5 - - + +
242G ILE* 5.0 0.2 - - + -
245G ILE* 3.5 33.2 - - + -
421G ALA 3.4 12.8 + - - +
422G LEU 3.3 4.3 + - - +
424G ASP* 1.3 76.6 - - - +
426G LYS* 1.3 60.9 + - - +
428G ALA* 3.4 1.8 + - - +
429G LEU* 2.8 37.6 + - + +
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Residues in contact with LYS 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398G ILE* 5.4 5.5 - - + +
401G CYS* 4.1 28.6 - - + -
402G ASN* 3.5 19.1 + - - +
405G GLU* 3.2 35.5 + - - +
422G LEU* 3.1 16.1 + - + +
423G ALA* 3.8 5.4 - - - +
425G ALA* 1.3 73.2 - - - +
427G ALA* 1.3 62.0 + - - +
429G LEU* 3.0 5.6 + - - +
430G GLU* 2.7 63.8 + - + +
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Residues in contact with ALA 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G ALA 3.0 17.7 + - - +
424G ASP* 3.8 4.9 - - - +
426G LYS* 1.3 76.8 - - - +
428G ALA* 1.3 63.3 + - - +
430G GLU* 3.2 7.7 + - - +
431G ALA* 3.1 24.7 + - - +
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Residues in contact with ALA 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G ILE* 4.7 14.1 - - + -
182G PRO* 4.8 12.0 - - + +
424G ASP 2.9 20.3 + - - +
425G ALA* 3.6 7.2 - - - +
427G ALA* 1.3 77.1 - - - +
429G LEU* 1.3 60.9 + - - +
431G ALA* 3.5 12.4 + - - +
432G LEU* 3.4 19.6 - - - +
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Residues in contact with LEU 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G ILE* 3.7 26.9 - - + +
182G PRO* 6.3 0.2 - - + -
185G LEU* 3.8 30.1 - - + -
245G ILE* 4.4 4.9 - - + -
249G ILE* 5.3 0.7 - - + -
394G LYS* 3.9 14.1 + - + +
397G ALA* 3.7 41.3 - - + -
398G ILE* 4.0 16.8 - - + +
401G CYS* 4.3 11.4 - - - -
425G ALA* 2.8 29.1 + - + +
426G LYS 3.0 3.3 + - - +
428G ALA* 1.3 75.1 - - - +
430G GLU* 1.3 59.8 - - - +
432G LEU* 3.4 27.1 + - + +
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Residues in contact with GLU 430 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398G ILE* 4.1 28.1 - - + +
426G LYS* 2.7 65.5 + - + +
427G ALA* 3.8 6.7 + - - +
429G LEU* 1.3 75.3 - - - +
431G ALA* 1.3 63.9 + - - +
432G LEU 3.2 7.7 + - - +
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Residues in contact with ALA 431 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G ALA 3.1 15.3 + - - +
428G ALA* 3.8 9.0 - - - +
429G LEU 3.3 0.4 - - - -
430G GLU* 1.3 78.4 - - - +
432G LEU* 1.3 62.0 + - + +
433G PRO* 3.9 1.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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