Contacts of the helix formed by residues 450 - 455 (chain G) in PDB entry 4IG9
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 LEU 450 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446G ARG* 3.4 52.7 - - + +
447G PRO* 3.0 15.6 + - + +
449G ALA* 1.3 80.7 - - + +
451G ILE* 1.3 65.0 + - - +
452G PRO 3.5 0.7 - - - -
453G SER* 3.5 13.1 + - - +
454G SER* 3.1 23.7 + - - -
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Residues in contact with ILE 451 (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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257G ILE* 5.0 4.9 - - + -
259G LEU* 3.8 25.6 - - + -
343G TYR* 3.8 32.1 - - + -
422G PHE* 4.0 17.0 - - + -
426G MET* 4.0 24.2 - - + -
436G LEU* 4.8 6.1 - - + -
447G PRO 4.0 4.0 - - - +
448G VAL* 3.3 28.7 - - + +
450G LEU* 1.3 75.7 - - - +
452G PRO* 1.4 68.4 - - + +
454G SER* 2.9 20.4 + - - -
455G ILE* 3.5 16.7 + - + +
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Residues in contact with PRO 452 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234G ARG* 4.7 6.1 - - - +
259G LEU* 4.0 10.3 - - + -
436G LEU* 3.8 11.0 - - + -
438G VAL* 4.9 1.8 - - + -
443G LEU* 3.9 25.6 - - + -
448G VAL 3.5 9.0 - - - +
449G ALA* 3.7 10.3 - - - +
450G LEU 3.7 2.7 - - - -
451G ILE* 1.4 94.3 - - + +
453G SER* 1.3 59.6 + - - +
455G ILE* 3.6 8.8 - - + +
461G GLN* 2.9 42.8 + - - +
472G LEU* 4.6 15.0 - - + -
474G PHE* 5.1 0.4 - - + -
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Residues in contact with SER 453 (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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-1G MET* 5.1 10.4 - - - -
234G ARG* 5.9 4.9 - - - +
449G ALA 4.9 4.9 + - - -
450G LEU* 3.5 14.6 + - - +
451G ILE 3.1 0.8 - - - -
452G PRO* 1.3 77.5 - - - +
454G SER* 1.3 62.1 + - - +
455G ILE 3.3 7.4 + - - +
457G HIS* 4.7 11.5 - - - -
472G LEU* 4.7 13.9 - - - +
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Residues in contact with SER 454 (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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426G MET* 3.3 23.4 - - - +
430G LYS* 3.8 25.8 + - - +
450G LEU* 3.1 15.3 + - - -
451G ILE* 2.9 15.6 + - - -
453G SER* 1.3 79.1 - - - +
455G ILE* 1.3 58.9 + - - +
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Residues in contact with ILE 455 (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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234G ARG* 5.7 0.2 - - - -
257G ILE* 5.2 5.2 - - + -
426G MET* 4.4 12.6 - - + -
430G LYS* 4.5 6.5 - - - -
433G VAL* 4.1 19.3 - - + -
436G LEU* 3.7 30.3 - - + -
451G ILE* 3.5 17.5 - - + +
452G PRO 3.6 16.5 - - - +
453G SER 3.9 7.6 - - - +
454G SER* 1.3 84.5 - - - +
456G PRO* 1.3 76.2 - - + +
457G HIS* 3.5 8.5 + - - -
459G VAL* 4.2 20.6 - - + -
461G GLN* 3.6 19.2 + - - +
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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