Contacts of the helix formed by residues 484 - 491 (chain B) in PDB entry 5I4V
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 GLY 484 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A GLU* 5.5 9.4 + - - -
404A LEU* 5.8 3.4 - - - -
482B GLN 3.2 1.0 - - - -
483B GLN* 1.3 80.4 - - - +
485B ARG* 1.3 57.5 + - - +
486B PHE 3.4 2.0 - - - -
487B ALA* 3.5 12.2 + - - +
488B LYS* 3.0 34.5 + - - +
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Residues in contact with ARG 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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431B MET* 2.7 35.1 + - - +
432B ARG 3.0 22.8 + - - -
433B MET* 3.6 2.4 - - - +
437B GLU* 2.6 45.3 + - - +
475B CYS* 4.2 15.0 - - + -
479B TYR* 3.8 35.9 - - + -
482B GLN* 3.2 47.6 + - + +
483B GLN 3.5 1.0 - - - -
484B GLY* 1.3 75.4 - - - +
486B PHE* 1.3 66.8 + - - +
488B LYS* 3.2 13.5 + - + +
489B LEU* 3.0 26.9 + - + +
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Residues in contact with PHE 486 (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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418A PHE* 4.6 12.1 - + - -
419A PRO* 4.1 25.1 - - + -
468B TYR* 3.6 29.4 - - - -
471B LEU* 3.8 24.5 - - + -
472B GLU* 3.3 51.8 - - + +
475B CYS* 4.1 20.4 - - + +
476B LYS* 6.5 0.4 - - + -
483B GLN 5.2 2.6 + - - +
484B GLY 5.2 0.2 - - - -
485B ARG* 1.3 78.4 - - - +
487B ALA* 1.3 63.5 + - - +
489B LEU* 3.2 6.5 + - - +
490B LEU* 3.2 48.3 + - + +
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Residues in contact with ALA 487 (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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400A VAL* 4.0 17.9 - - + -
404A LEU* 6.0 3.1 - - + -
418A PHE* 4.0 28.9 - - + -
422A LEU* 4.3 9.9 - - + -
484B GLY* 3.5 13.7 + - - +
485B ARG 3.3 0.6 - - - -
486B PHE* 1.3 76.3 - - - +
488B LYS* 1.3 65.2 + - - +
490B LEU* 3.2 3.5 + - - +
491B LEU* 2.9 32.3 + - + +
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Residues in contact with LYS 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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397A GLN* 5.3 9.0 - - - -
431B MET* 3.4 38.3 - - + +
482B GLN* 5.7 4.4 + - - +
484B GLY 3.0 17.4 + - - +
485B ARG* 3.2 16.4 + - + +
487B ALA* 1.3 77.4 - - - +
489B LEU* 1.3 62.3 + - - +
491B LEU* 3.6 15.6 + - + +
492B ARG* 3.7 9.0 + - - +
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Residues in contact with LEU 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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431B MET* 3.7 26.7 - - - -
433B MET* 4.0 25.4 - - + -
437B GLU* 3.9 27.8 - - + +
441B LEU* 3.9 25.0 - - + +
471B LEU* 4.0 15.5 - - + -
475B CYS* 3.6 31.4 - - - -
485B ARG* 3.0 18.8 + - + +
486B PHE* 3.5 7.4 - - - +
488B LYS* 1.3 74.3 - - - +
490B LEU* 1.3 65.5 + - - +
492B ARG* 3.1 21.8 + - - +
493B LEU* 4.1 0.5 - - - +
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Residues in contact with LEU 490 (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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419A PRO* 3.8 26.7 - - + +
422A LEU* 4.3 23.6 - - + -
423A MET* 4.6 12.9 - - - +
426A VAL* 5.3 0.2 - - - +
441B LEU* 4.2 10.5 - - + -
444B ILE* 3.9 28.0 - - + -
468B TYR* 4.8 2.9 - - + -
471B LEU* 4.5 1.8 - - + -
486B PHE* 3.2 45.6 + - + +
487B ALA 3.2 5.8 + - - +
489B LEU* 1.3 78.6 - - - +
491B LEU* 1.3 58.3 + - - +
493B LEU* 3.0 35.1 + - + +
494B PRO* 3.4 3.6 - - - +
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Residues in contact with LEU 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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376A ILE* 4.8 2.2 - - + -
396A GLN* 3.7 31.9 - - - +
400A VAL* 4.1 22.2 - - + -
422A LEU* 4.4 20.0 - - + +
425A LEU* 4.2 24.9 - - + -
487B ALA* 2.9 25.7 + - + +
488B LYS* 4.0 10.1 - - + +
489B LEU 3.2 0.6 - - - -
490B LEU* 1.3 72.9 - - - +
492B ARG* 1.3 80.8 + - - +
493B LEU 3.3 0.7 - - - -
494B PRO* 3.5 16.3 - - + +
495B ALA* 4.5 3.5 + - - +
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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