Contacts of the strand formed by residues 438 - 445 (chain B) in PDB entry 5DQE
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 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B HIS 5.5 0.7 - - - -
302B PHE* 3.5 7.1 - - - -
303B TRP* 2.7 54.0 + - + +
435B ARG* 2.7 37.7 + - - +
436B GLY 4.5 4.2 - - - +
437B ALA* 1.3 76.2 - - - +
439B HIS* 1.3 72.2 + - + +
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Residues in contact with HIS 439 (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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253B HIS 3.1 27.4 + - - -
254B ILE* 4.1 19.7 - - + +
255B SER 5.0 3.2 + - - -
256B GLN* 6.2 0.2 - - + -
300B VAL* 4.1 4.9 - - + -
301B LYS 3.0 12.8 - - - +
302B PHE* 3.5 18.2 - - + -
303B TRP* 4.1 5.9 - - - -
438B GLN* 1.3 88.1 - - + +
440B HIS* 1.3 62.5 + - - +
441B ILE* 3.6 34.1 - - + +
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Residues in contact with HIS 440 (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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267B GLU* 3.3 31.9 + - + -
299B LEU 3.8 1.2 - - - +
300B VAL* 3.5 2.3 - - - -
301B LYS* 2.8 34.6 + - + +
303B TRP* 4.1 18.6 - + + -
439B HIS* 1.3 76.9 - - - +
441B ILE* 1.3 72.8 + - - +
442B TYR* 3.1 41.7 + + + +
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Residues in contact with ILE 441 (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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222B GLY* 5.6 0.4 - - - -
223B LEU* 4.2 28.7 - - + +
254B ILE* 4.5 8.5 - - + -
256B GLN* 3.7 23.6 - - + +
266B LEU* 3.7 43.1 - - + +
267B GLU 4.7 0.9 + - - -
298B PHE* 4.4 2.7 - - + -
299B LEU 3.6 6.5 - - - +
300B VAL* 4.3 13.5 - - + +
439B HIS* 3.6 32.5 - - + +
440B HIS* 1.3 88.6 + - - +
442B TYR* 1.3 68.0 + - - +
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Residues in contact with TYR 442 (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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266B LEU* 4.3 4.9 - - - -
267B GLU* 3.2 44.0 + - + +
268B SER 4.3 0.9 - - - -
269B VAL* 3.6 26.5 - - + -
298B PHE* 3.4 8.5 - - - +
299B LEU* 2.8 54.1 + - + +
301B LYS* 3.6 41.3 + - + +
303B TRP* 6.0 0.3 - - - -
440B HIS* 3.1 41.5 + + - +
441B ILE* 1.3 72.2 - - - +
443B ARG* 1.3 64.2 + - - +
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Residues in contact with ARG 443 (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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220B ALA* 3.7 45.3 + - + +
265B PRO* 4.2 12.9 - - - +
266B LEU* 2.5 35.9 + - + +
267B GLU* 2.8 12.8 + - - +
268B SER* 3.3 10.7 - - - +
269B VAL* 2.9 25.6 + - - -
295B HIS 5.9 1.1 - - - +
297B PHE 3.8 5.8 - - - +
298B PHE* 4.2 11.7 - - + -
442B TYR* 1.3 73.7 - - - +
444B LEU* 1.3 61.7 + - - +
445B VAL* 4.2 21.6 - - + +
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Residues in contact with LEU 444 (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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269B VAL* 3.3 22.0 - - + +
271B VAL* 3.8 29.6 - - + +
274B ILE* 3.8 30.5 - - + -
285B LEU* 4.6 7.9 - - + -
289B TYR* 3.1 15.7 + - + -
294B PRO 4.1 5.9 - - - +
297B PHE* 2.8 30.9 + - + +
298B PHE 3.5 25.8 - - - +
299B LEU* 3.9 20.2 - - + -
423B CYS* 5.5 0.4 - - - +
425B ALA* 4.4 6.5 - - + +
442B TYR 3.8 0.6 + - - -
443B ARG* 1.3 73.6 - - - +
445B VAL* 1.3 62.8 + - - +
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Residues in contact with VAL 445 (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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268B SER* 3.8 34.3 - - - +
269B VAL 2.9 17.6 + - - +
270B ASP* 3.3 13.8 - - + +
271B VAL* 2.9 24.6 + - - +
289B TYR* 3.4 6.5 - - - -
443B ARG* 4.1 21.3 - - + +
444B LEU* 1.3 79.7 - - - +
446B ARG* 1.3 65.0 + - - +
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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