Contacts of the helix formed by residues 484 - 498 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394B GLU* 6.0 2.0 - - - +
401B ILE* 4.2 4.3 - - - -
482B ARG 4.7 4.9 - - - +
483B LEU* 1.3 78.7 - - - +
485B ALA* 1.3 65.4 + - - +
486B LEU* 3.8 6.5 + - - +
487B ARG* 3.0 27.7 + - + +
488B ILE* 3.0 24.4 + - - +
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Residues in contact with ALA 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ALA* 4.4 5.4 - - - +
313B LEU* 3.9 10.8 - - + +
314B ALA* 3.5 33.3 - - + +
317B HIS* 4.1 12.6 + - + +
401B ILE* 3.6 23.7 - - + +
404B MET* 5.7 2.2 - - - -
484B THR* 1.3 72.7 - - - +
486B LEU* 1.3 58.0 + - - +
487B ARG 3.2 0.2 + - - -
488B ILE* 3.2 7.6 + - - +
489B LYS* 2.9 29.3 + - - +
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Residues in contact with LEU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ALA* 4.0 11.1 - - + +
318B MET* 3.6 31.2 - - + -
484B THR* 3.2 6.8 + - - +
485B ALA* 1.3 78.5 - - - +
487B ARG* 1.3 57.3 + - - +
489B LYS* 3.4 18.6 + - + +
490B LYS* 2.9 56.8 + - - +
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Residues in contact with ARG 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 3.6 28.7 - - + -
484B THR* 3.0 31.7 + - + +
486B LEU* 1.3 76.8 - - - +
488B ILE* 1.3 61.5 + - - +
490B LYS* 3.0 48.1 + - - +
491B THR* 2.9 45.3 + - + +
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Residues in contact with ILE 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ALA* 4.1 8.3 - - + -
401B ILE* 4.3 9.9 - - + -
404B MET* 4.6 13.9 - - - -
408B PHE* 3.8 26.5 - - + -
470B ILE* 3.7 21.5 - - + -
474B CYS* 3.7 30.5 - - - -
483B LEU* 3.9 20.2 - - + -
484B THR 3.0 15.0 + - - +
485B ALA* 3.7 6.3 - - - +
487B ARG* 1.3 75.2 - - - +
489B LYS* 1.3 57.6 + - - +
491B THR* 3.9 6.6 + - - -
492B LEU* 2.8 40.3 + - + +
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Residues in contact with LYS 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B HIS* 5.4 5.5 - - - -
307B LEU* 4.0 6.5 - - + +
310B ALA* 4.1 15.2 - - + +
311B SER* 3.5 36.9 + - - +
314B ALA* 4.5 13.9 - - + +
485B ALA 2.9 18.3 + - - +
486B LEU* 3.5 22.0 - - + +
488B ILE* 1.3 75.8 - - - +
490B LYS* 1.3 58.6 + - - +
492B LEU* 3.9 1.7 - - - -
493B SER* 2.9 35.1 + - - -
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Residues in contact with LYS 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B LEU* 2.9 38.7 + - - +
487B ARG* 3.0 39.8 + - - +
489B LYS* 1.3 78.8 - - - +
491B THR* 1.3 57.7 + - - +
493B SER* 3.1 7.5 + - - -
494B GLN* 3.0 29.8 + - - +
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Residues in contact with THR 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B VAL* 4.3 11.3 - - - +
470B ILE* 4.0 19.3 - - + +
483B LEU* 6.0 3.4 - - + -
487B ARG* 2.9 43.3 + - + +
488B ILE* 3.9 4.3 + - - -
490B LYS* 1.3 74.3 - - - +
492B LEU* 1.3 57.8 + - - +
494B GLN* 3.3 9.5 - - - +
495B LEU* 3.1 25.1 + - - +
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ILE* 4.2 9.0 - - + +
306B ALA* 3.4 44.0 - - + +
307B LEU* 3.5 16.7 - - + +
310B ALA* 4.5 1.3 - - + -
408B PHE* 3.8 14.4 - - + -
466B VAL* 4.5 10.8 - - + -
467B MET* 4.2 13.5 - - - -
470B ILE* 3.6 22.4 - - + -
488B ILE* 2.8 22.2 + - + +
489B LYS* 4.1 2.7 - - - +
491B THR* 1.3 76.5 + - - +
493B SER* 1.3 65.5 + - - +
494B GLN 3.1 0.4 - - - -
495B LEU* 3.6 13.4 + - + +
496B SER* 3.3 20.4 + - - -
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Residues in contact with SER 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 4.2 19.7 - - - +
489B LYS* 2.9 25.6 + - - -
490B LYS* 3.3 8.3 - - - -
492B LEU* 1.3 76.6 - - - +
494B GLN* 1.3 64.1 - - - +
496B SER* 3.4 9.5 + - - -
497B GLN* 3.4 18.0 + - - +
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Residues in contact with GLN 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490B LYS* 3.0 14.1 + - - +
491B THR* 3.3 13.9 - - - +
493B SER* 1.3 73.9 - - - +
495B LEU* 1.3 64.0 + - - +
496B SER 2.8 5.8 + - - -
497B GLN* 3.0 23.7 + - - +
498B GLN* 3.2 32.4 + - + +
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Residues in contact with LEU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ILE* 3.9 18.6 - - + -
462B GLU* 4.0 26.2 - - + -
463B ALA* 3.7 30.1 - - + +
466B VAL* 3.7 26.2 - - + -
467B MET* 5.4 2.9 - - + -
491B THR 3.1 12.2 + - - +
492B LEU* 3.8 16.6 - - + +
493B SER 3.5 0.2 - - - -
494B GLN* 1.3 78.7 - - - +
496B SER* 1.3 59.3 + - - +
498B GLN* 3.6 10.0 + - + +
499B GLU* 3.0 44.8 + - + +
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Residues in contact with SER 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ILE* 4.0 15.3 - - - +
307B LEU* 4.6 11.4 - - - +
492B LEU 3.3 11.8 + - - -
493B SER* 3.4 12.8 - - - -
494B GLN 2.8 2.2 + - - -
495B LEU* 1.3 78.2 - - - +
497B GLN* 1.3 64.9 + - - -
499B GLU* 3.1 14.1 + - - +
501B ILE* 3.3 43.2 + - - +
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Residues in contact with GLN 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B SER* 3.4 11.0 + - - +
494B GLN* 3.0 17.7 + - - +
496B SER* 1.3 73.7 - - - +
498B GLN* 1.3 65.3 + - - +
499B GLU 3.0 5.2 - - - -
500B GLY* 3.1 18.5 + - - +
501B ILE 5.0 3.4 - - - +
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Residues in contact with GLN 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B GLN* 3.2 28.4 + - + +
495B LEU* 3.8 14.4 - - + +
496B SER 3.2 0.4 - - - -
497B GLN* 1.3 82.7 - - - +
499B GLU* 1.3 64.2 + - + +
500B GLY 3.4 0.2 - - - -
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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