Contacts of the strand formed by residues 496 - 501 (chain D) in PDB entry 3GEB
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 VAL 496 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A MET* 4.0 22.9 - - + -
268D GLU 3.2 5.2 + - - +
269D ARG* 3.3 38.7 - - + +
270D VAL* 3.0 22.2 + - - +
494D LYS 4.3 6.5 - - - +
495D ALA* 1.3 78.5 - - - +
497D TYR* 1.3 61.0 + - - +
498D VAL* 3.9 4.8 + - + -
516D PRO* 5.5 3.8 - - + -
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Residues in contact with TYR 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D VAL* 3.3 39.0 - - + +
272D VAL* 4.6 7.2 - - + -
487D ILE* 3.9 23.3 - - + -
488D MET* 3.3 43.2 + - + -
491D PHE* 3.1 21.2 - + + +
492D GLY 2.6 28.5 + - - -
493D ARG* 5.4 1.6 - - - -
495D ALA* 3.4 23.7 - - + +
496D VAL* 1.3 73.7 - - - +
498D VAL* 1.3 61.2 + - - +
499D VAL 3.9 0.4 - - - -
515D MET* 3.6 25.9 - - + +
516D PRO* 3.2 28.4 - - - +
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Residues in contact with VAL 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A MET* 4.9 2.5 - - + -
269D ARG* 4.8 4.7 - - + -
270D VAL 2.9 10.1 + - - +
271D PHE* 3.3 40.6 - - + -
272D VAL* 2.8 26.3 + - - +
496D VAL* 4.7 14.8 - - + +
497D TYR* 1.3 73.7 - - - +
499D VAL* 1.3 62.5 + - - +
500D ILE* 3.7 10.3 + - + +
516D PRO* 3.6 15.9 - - + +
518D TRP* 3.8 29.4 - - + -
538D LEU* 4.3 15.0 - - + -
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Residues in contact with VAL 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D VAL* 3.5 17.3 - - + +
484D PHE* 3.8 29.2 - - + -
497D TYR 4.7 0.4 - - - +
498D VAL* 1.3 73.0 - - - +
500D ILE* 1.3 64.2 + - - +
506D GLU* 3.9 13.7 - - + +
510D ALA* 3.4 27.4 - - + -
515D MET* 3.9 25.1 - - + -
516D PRO 2.9 9.0 + - - +
517D PHE* 3.3 20.5 - - + -
518D TRP* 2.9 26.0 + - - +
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Residues in contact with ILE 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D PHE* 3.9 25.8 - - + -
272D VAL 3.0 9.5 + - - +
273D TRP* 3.7 47.0 - - + -
274D ASP* 3.2 25.3 + - - +
278D THR* 3.9 2.5 - - + +
435D ILE* 5.3 0.2 - - + -
498D VAL* 3.8 13.2 - - + +
499D VAL* 1.3 80.4 - - - +
501D GLY* 1.3 59.7 + - - +
506D GLU* 5.1 0.5 - - - +
517D PHE* 4.4 0.7 - - - -
518D TRP* 3.7 11.4 - - + +
520D ILE* 3.3 33.9 - - + -
529D LEU* 3.8 17.9 - - + -
533D LEU* 6.1 0.4 - - + -
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Residues in contact with GLY 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ASP* 3.9 4.0 - - - -
278D THR* 3.7 10.5 - - - -
500D ILE* 1.3 76.0 - - - +
502D ASP* 1.3 61.0 + - - -
503D GLY 3.6 1.1 - - - -
506D GLU* 3.7 13.2 - - - -
517D PHE* 3.3 26.6 - - - -
518D TRP 3.3 6.1 + - - +
519D ARG* 3.5 0.5 - - - -
520D ILE* 3.0 21.5 + - - -
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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