Contacts of the strand formed by residues 490 - 494 (chain B) in PDB entry 4N41
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 ALA 490 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B PHE* 3.5 2.6 - - - -
478B ASP 2.9 29.2 + - - -
489B GLY* 1.3 75.7 - - - +
491B ALA* 1.3 65.7 + - - +
504B THR 3.8 4.9 - - - +
505B LEU* 4.0 10.5 - - + -
522B LEU* 3.7 15.8 - - - +
659B ALA* 4.8 3.1 - - - +
662B LEU* 3.8 21.5 - - + -
663B VAL* 3.7 22.9 - - + -
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Residues in contact with ALA 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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475B VAL* 4.0 17.3 - - + -
476B GLY 3.2 11.4 - - - +
477B PHE* 4.3 5.6 - - + -
490B ALA* 1.3 78.2 - - - +
492B CYS* 1.3 70.2 + - - +
504B THR* 2.9 47.7 + - - +
522B LEU* 4.2 14.1 - - + -
526B THR* 4.2 4.3 - - - +
659B ALA* 4.6 1.6 - - - -
662B LEU* 3.7 1.9 - - - +
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Residues in contact with CYS 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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475B VAL* 3.3 5.1 - - - +
476B GLY 2.9 31.0 + - - -
491B ALA* 1.3 84.1 - - - +
493B ALA* 1.3 63.0 + - - +
502B LEU 3.2 8.5 - - - +
503B TRP* 4.1 5.4 - - - -
504B THR* 4.9 0.9 - - - +
526B THR* 5.6 0.7 - - - -
655B PRO* 3.5 21.0 - - - +
658B LEU* 3.5 26.0 - - + -
659B ALA* 3.4 23.1 - - - -
662B LEU* 3.8 14.1 - - - -
682B LEU* 6.3 0.2 - - - -
684B PHE* 3.9 10.8 - - - -
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Residues in contact with ALA 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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473B LEU* 4.1 12.1 - - + -
474B ALA 3.0 12.1 - - - +
475B VAL* 4.1 4.9 - - + -
492B CYS* 1.3 77.5 - - - +
494B VAL* 1.3 65.1 + - - +
500B HIS 3.7 0.6 - - - +
501B LEU* 3.4 6.8 - - - +
502B LEU* 2.9 40.4 + - + +
526B THR* 3.6 29.6 - - + -
655B PRO* 4.6 0.8 - - - +
658B LEU* 5.3 2.0 - - - +
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Residues in contact with VAL 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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461B GLN* 5.2 3.6 - - - +
472B GLU 3.8 7.5 - - - +
473B LEU* 3.5 18.8 - - - -
474B ALA* 2.9 32.4 + - + +
493B ALA* 1.3 76.8 - - - +
500B HIS 3.4 17.0 - - - +
501B LEU* 3.4 27.1 - - + -
502B LEU* 6.2 0.4 - - - -
530B PHE* 6.0 1.1 - - - -
638B LEU* 4.3 13.9 - - + -
641B LEU* 3.5 28.9 - - + -
654B ALA* 4.6 4.9 - - + -
655B PRO* 3.8 28.5 - - + -
658B LEU* 5.1 2.0 - - + -
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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