Contacts of the strand formed by residues 491 - 495 (chain B) in PDB entry 4CH9
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 GLN 491 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B VAL* 4.7 0.7 - - - -
487B VAL* 3.2 7.4 - - - +
488B LEU 3.0 32.6 + - - +
489B SER* 3.6 14.4 + - - +
490B GLY* 1.3 101.4 + - - +
492B LEU* 1.3 61.2 + - - +
493B TYR* 3.6 11.8 - - + +
509B VAL* 3.5 22.0 - - + +
510B TYR 3.6 4.1 - - - +
511B ASP* 3.4 39.6 + - - +
512B PRO* 4.4 0.2 - - - +
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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
----------------------------------------------------------
437B GLY* 3.9 14.1 - - - +
439B VAL* 4.5 9.4 - - + +
444B TYR* 3.7 35.7 - - + -
446B VAL* 3.9 16.4 - - + -
460B VAL* 5.0 0.4 - - + -
485B VAL* 3.8 26.5 - - + -
486B GLY 3.6 7.0 - - - +
487B VAL* 3.8 15.7 - - + -
490B GLY 4.4 0.2 + - - -
491B GLN* 1.3 71.4 - - - +
493B TYR* 1.3 61.5 + - - +
509B VAL* 3.3 3.2 - - - -
510B TYR* 2.8 56.6 + - + +
512B PRO* 5.1 1.1 - - + +
517B TRP* 3.6 16.2 - - + -
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Residues in contact with TYR 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B VAL* 3.2 30.2 - - - +
486B GLY 2.8 19.7 + - - +
488B LEU* 3.7 32.3 + - + +
491B GLN* 3.6 19.3 - - + +
492B LEU* 1.3 73.9 - - - +
494B ALA* 1.3 61.2 + - - +
495B THR* 4.0 5.2 - - + -
507B VAL* 4.2 15.7 - - + -
508B GLU 3.6 1.3 - - - -
509B VAL* 3.6 33.0 - - + +
517B TRP* 4.8 0.2 - - - -
520B VAL* 4.7 4.4 - - + +
539B LEU* 3.7 27.8 - - + -
557B TYR* 3.6 28.4 - + - -
559B PRO* 3.5 26.6 - - + +
564B TRP* 5.8 0.2 - + - -
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Residues in contact with ALA 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B VAL* 3.9 11.4 - - + -
476B MET* 3.6 31.2 - - - -
480B ARG* 4.1 13.5 - - - +
483B ALA* 4.8 0.9 - - + -
484B GLY 3.9 2.2 - - - -
485B VAL* 4.4 4.0 - - + -
492B LEU 4.0 0.6 + - - -
493B TYR* 1.3 73.8 - - - +
495B THR* 1.3 60.3 + - - +
507B VAL* 3.5 2.8 - - - +
508B GLU* 2.9 32.6 + - + +
517B TRP* 3.9 13.5 - - + -
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Residues in contact with THR 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ALA* 3.4 2.1 - - - +
484B GLY* 2.8 60.1 + - - +
493B TYR* 4.5 2.9 - - + -
494B ALA* 1.3 75.7 - - - +
496B GLY* 1.3 67.4 + - - +
497B GLY 3.4 0.2 + - - -
506B SER 4.0 3.4 - - - -
507B VAL* 3.9 19.5 - - + -
523B MET* 4.0 17.5 - - - +
527B ARG 4.7 0.3 - - - +
530B ALA* 5.6 0.5 - - - +
532B VAL* 4.3 0.4 - - + +
539B LEU* 4.2 16.4 - - + -
541B VAL* 4.1 13.7 - - + +
564B TRP* 4.0 19.3 - - + -
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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
------------------------------------------------------------
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