Contacts of the helix formed by residues 484 - 496 (chain C) in PDB entry 1IAS
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 484 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394C GLU* 6.0 1.8 - - - +
401C ILE* 4.2 4.0 - - - -
482C ARG 4.7 5.2 - - - +
483C LEU* 1.3 78.9 - - - +
485C ALA* 1.3 65.0 + - - +
486C LEU* 3.9 6.9 + - - +
487C ARG* 3.0 26.3 + - + +
488C ILE* 3.0 24.9 + - - +
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Residues in contact with ALA 485 (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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310C ALA* 4.4 4.8 - - - +
313C LEU* 3.9 12.3 - - + +
314C ALA* 3.5 33.0 - - + +
317C HIS* 4.1 11.7 + - + +
401C ILE* 3.6 22.4 - - + +
404C MET* 5.7 2.0 - - - -
484C THR* 1.3 73.0 - - - +
486C LEU* 1.3 57.9 + - - +
488C ILE* 3.2 8.4 + - - +
489C LYS* 2.8 29.1 + - - +
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Residues in contact with LEU 486 (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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314C ALA* 4.1 10.4 - - + +
318C MET* 3.7 31.0 - - + -
484C THR* 3.3 6.6 + - - +
485C ALA* 1.3 78.8 - - - +
487C ARG* 1.3 56.4 + - - +
489C LYS* 3.3 19.9 + - + +
490C LYS* 2.9 57.0 + - - +
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Residues in contact with ARG 487 (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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483C LEU* 3.6 28.7 - - + -
484C THR* 3.0 31.9 + - - +
486C LEU* 1.3 77.6 - - - +
488C ILE* 1.3 63.7 + - - +
490C LYS* 3.0 56.4 + - - +
491C THR* 2.9 37.4 + - + +
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Residues in contact with ILE 488 (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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310C ALA* 4.2 8.5 - - + -
401C ILE* 4.3 10.1 - - + -
404C MET* 4.6 14.4 - - - -
408C PHE* 3.7 26.7 - - + -
470C ILE* 3.7 23.3 - - + -
474C CYS* 3.7 30.3 - - - -
483C LEU* 3.9 18.6 - - + -
484C THR 3.0 15.5 + - - +
485C ALA* 3.7 5.8 - - - +
487C ARG* 1.3 74.8 - - - +
489C LYS* 1.3 58.3 + - - +
491C THR* 4.0 6.4 + - - -
492C LEU* 2.9 40.9 + - + +
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Residues in contact with LYS 489 (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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256C HIS* 5.7 4.4 - - - -
307C LEU* 3.9 9.5 - - + +
310C ALA* 4.1 18.5 - - + +
311C SER* 3.4 38.1 + - - +
314C ALA* 4.5 9.9 - - + -
485C ALA 2.8 17.4 + - - +
486C LEU* 3.4 22.7 - - + +
487C ARG 3.2 0.2 - - - -
488C ILE* 1.3 74.1 - - - +
490C LYS* 1.3 59.3 + - - +
492C LEU* 4.6 0.2 - - - -
493C SER* 2.9 35.5 + - - -
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Residues in contact with LYS 490 (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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486C LEU* 2.9 39.5 + - - +
487C ARG* 3.0 38.1 + - - +
489C LYS* 1.3 77.7 - - - +
491C THR* 1.3 58.2 + - - +
493C SER* 3.1 8.4 + - - -
494C GLN* 3.0 30.8 + - - +
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Residues in contact with THR 491 (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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466C VAL* 4.3 10.9 - - - +
470C ILE* 4.0 19.4 - - + +
483C LEU* 6.0 3.6 - - + -
487C ARG* 2.9 43.0 + - + +
488C ILE* 4.0 3.8 + - - -
490C LYS* 1.3 75.1 - - - +
492C LEU* 1.3 58.5 + - - +
494C GLN* 3.3 8.3 - - - +
495C LEU* 3.1 25.3 + - - +
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Residues in contact with LEU 492 (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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303C ILE* 4.1 8.3 - - + +
306C ALA* 3.5 44.2 - - + +
307C LEU* 3.5 13.4 - - + +
310C ALA* 4.6 1.3 - - + -
408C PHE* 3.8 15.0 - - + -
466C VAL* 4.5 11.4 - - + -
467C MET* 4.2 13.7 - - - -
470C ILE* 3.6 22.7 - - + -
488C ILE* 2.9 22.2 + - + +
489C LYS* 4.0 2.9 - - - +
491C THR* 1.3 76.8 + - - +
493C SER* 1.3 64.6 + - - +
494C GLN 3.1 0.4 - - - -
495C LEU* 3.6 12.7 + - + +
496C SER* 3.1 24.8 + - - -
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Residues in contact with SER 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C LEU* 4.2 19.7 - - - +
489C LYS* 2.9 25.6 + - - -
490C LYS* 3.3 9.0 - - - -
492C LEU* 1.3 76.6 - - - +
494C GLN* 1.3 64.3 + - - +
496C SER* 3.6 2.7 + - - -
497C GLN* 3.1 26.4 + - - +
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Residues in contact with GLN 494 (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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490C LYS* 3.0 14.7 + - - +
491C THR* 3.3 13.7 - - - +
492C LEU 3.1 0.2 - - - -
493C SER* 1.3 75.9 - - - +
495C LEU* 1.3 56.9 + - - +
497C GLN* 2.7 65.5 + - - +
498C GLN* 3.0 24.3 + - + +
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Residues in contact with LEU 495 (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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303C ILE* 3.8 17.9 - - + -
462C GLU* 3.9 26.7 - - + -
463C ALA* 3.7 30.1 - - + +
466C VAL* 3.7 26.0 - - + -
467C MET* 5.3 3.1 - - + -
491C THR 3.1 12.7 + - - +
492C LEU* 3.9 15.0 - - + +
493C SER 3.5 0.2 - - - -
494C GLN* 1.3 78.9 - - - +
496C SER* 1.3 58.5 + - - +
498C GLN* 3.1 34.3 + - + +
499C GLU* 4.1 18.3 + - - +
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Residues in contact with SER 496 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ILE* 3.2 33.9 - - - +
304C LYS* 5.5 4.7 + - - +
307C LEU* 4.4 14.4 - - - +
492C LEU 3.1 11.4 + - - -
493C SER 3.8 5.6 - - - -
494C GLN 3.2 0.2 - - - -
495C LEU* 1.3 79.4 - - - +
497C GLN* 1.3 59.6 + - - +
499C GLU* 3.8 5.0 + - - +
500C GLY 3.6 23.9 + - - -
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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