Contacts of the helix formed by residues 488 - 495 (chain B) in PDB entry 4OL0
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 MET 488 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420B PHE* 4.7 5.2 - - + -
448B ALA* 4.0 13.7 - - + -
459B LEU* 3.5 49.8 - - + +
462B VAL* 4.6 7.6 - - + -
463B LEU* 4.0 31.0 - - + +
466B VAL* 5.5 0.4 - - - -
484B LEU* 3.4 32.5 - - - +
485B VAL* 3.1 11.7 + - - +
487B GLU* 1.3 80.4 - - - +
489B SER* 1.3 58.8 + - - +
490B GLU* 3.2 3.6 - - - +
491B VAL* 3.0 20.8 + - + +
492B VAL* 2.9 28.0 + - - +
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Residues in contact with SER 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LYS* 4.4 1.7 - - - +
485B VAL 3.9 0.4 + - - -
486B GLY 2.8 21.0 + - - -
487B GLU 3.5 2.2 + - - -
488B MET* 1.3 78.1 - - - +
490B GLU* 1.3 52.5 + - - +
492B VAL* 3.3 11.1 + - - +
493B ASP* 2.7 34.5 + - - +
525B ASN* 3.1 10.9 + - - -
526B ILE* 3.2 28.8 + - - +
529B VAL* 3.7 30.8 - - - +
530B CYS* 3.7 2.4 - - - -
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Residues in contact with GLU 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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449B LYS* 3.7 25.9 + - + +
487B GLU 5.8 0.4 - - - +
488B MET* 3.2 1.5 - - - -
489B SER* 1.3 75.6 - - - +
491B VAL* 1.3 60.8 + - + +
493B ASP* 3.0 5.4 + - - +
494B ARG* 2.8 66.0 + - - +
529B VAL* 3.3 36.6 - - - +
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Residues in contact with VAL 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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448B ALA 5.8 2.7 - - - +
456B ASN* 5.1 3.8 - - + -
459B LEU* 3.7 42.6 - - + -
460B VAL* 4.2 19.3 - - + +
463B LEU* 4.3 10.7 - - + +
488B MET* 3.0 36.7 + - + +
490B GLU* 1.3 79.7 - - + +
492B VAL* 1.3 60.4 + - - +
494B ARG* 3.5 4.2 + - - +
495B ASN* 3.1 32.6 + - - +
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Residues in contact with VAL 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 3.8 25.8 - - + -
485B VAL 4.9 1.6 - - - +
488B MET 2.9 21.1 + - - +
489B SER* 3.5 11.0 - - - +
491B VAL* 1.3 77.9 - - - +
493B ASP* 1.3 61.5 + - - +
495B ASN 2.9 25.9 - - - +
496B PRO* 3.6 3.5 - - - +
498B PHE* 4.3 3.8 - - - +
499B LEU* 3.8 36.5 - - + +
502B VAL* 4.0 21.3 - - + -
526B ILE* 4.9 6.1 - - + -
530B CYS* 4.0 13.8 - - - -
533B HIS* 5.4 0.2 + - - -
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Residues in contact with ASP 493 (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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489B SER 2.7 17.9 + - - +
490B GLU* 3.0 11.8 + - - +
492B VAL* 1.3 75.6 - - - +
494B ARG* 1.3 72.2 + - - +
495B ASN 3.4 0.7 + - - -
496B PRO* 3.9 3.8 - - - +
529B VAL* 3.7 24.8 - - + +
530B CYS* 3.5 21.0 - - - -
533B HIS* 3.5 36.0 + - - -
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Residues in contact with ARG 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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453B PRO* 4.3 31.1 - - - +
456B ASN* 6.4 0.7 - - + -
490B GLU* 2.8 52.3 + - - +
491B VAL* 4.2 3.4 - - - +
493B ASP* 1.3 86.1 + - - +
495B ASN* 1.3 70.7 + - - +
496B PRO* 3.6 7.4 - - - +
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Residues in contact with ASN 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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456B ASN* 3.5 29.2 + - - +
460B VAL* 3.5 19.8 - - - +
491B VAL* 3.1 19.2 + - - +
492B VAL 2.9 10.6 - - - +
493B ASP 3.2 0.2 - - - -
494B ARG* 1.3 91.0 - - - +
496B PRO* 1.3 66.0 - - - +
497B GLN* 3.2 19.1 - - - +
498B PHE* 3.0 33.5 + - + +
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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