Contacts of the strand formed by residues 286 - 290 (chain D) in PDB entry 3COG
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 286 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D LEU* 3.3 47.7 - - + +
281D GLU* 5.1 1.8 - - - +
283D ASN* 3.2 23.7 + - + +
284D PRO 3.4 0.4 - - - -
285D TRP* 1.3 81.0 - - - +
287D GLU* 1.3 64.2 + - - +
288D LYS* 3.7 11.2 - - - +
289D VAL* 3.7 21.8 - - + -
316D PHE* 3.9 15.7 - - + -
317D TYR 3.8 8.5 - - - +
319D LYS* 3.9 10.0 + - - -
394D LEU* 4.1 7.9 - - + -
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Residues in contact with GLU 287 (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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286D VAL* 1.3 74.0 - - - +
288D LYS* 1.3 66.7 + - + +
317D TYR* 2.8 28.8 + - + +
318D ILE 4.3 2.5 - - - +
319D LYS* 3.6 37.1 - - + +
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Residues in contact with LYS 288 (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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286D VAL* 3.4 2.9 - - - +
287D GLU* 1.3 89.0 - - + +
289D VAL* 1.3 72.7 + - - +
290D ILE* 4.7 13.0 - - + +
298D PRO* 6.1 3.6 - - - +
316D PHE* 3.1 5.7 - - - +
317D TYR* 2.8 55.0 + - + +
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Residues in contact with VAL 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ALA* 3.9 9.0 - - + +
280D LEU* 3.7 7.2 - - + -
281D GLU* 3.5 40.4 + - + +
286D VAL* 3.7 14.8 - - + -
288D LYS* 1.3 85.1 - - - +
290D ILE* 1.3 68.3 + - - +
291D TYR 3.9 1.3 + - - -
294D LEU* 3.8 26.5 - - + -
296D SER* 4.3 13.9 + - - +
297D HIS* 5.7 1.0 + - - -
314D VAL* 4.0 19.1 - - + -
315D THR 3.6 10.1 - - - +
316D PHE* 4.2 2.7 - - + -
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Residues in contact with ILE 290 (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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163D THR* 3.3 35.0 - - - +
164D GLN* 3.6 13.0 + - + +
288D LYS* 4.7 16.8 - - + +
289D VAL* 1.3 76.2 - - - +
291D TYR* 1.3 60.5 + - - +
292D PRO* 4.5 0.4 - - - -
297D HIS* 3.6 27.4 - - + +
298D PRO* 5.6 3.8 - - + -
314D VAL* 4.2 0.3 - - - -
315D THR* 2.7 52.6 + - + +
317D TYR* 3.9 26.0 - - + +
373D LEU* 4.9 0.2 - - + -
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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