Contacts of the strand formed by residues 413 - 418 (chain B) in PDB entry 5FQD
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 LYS 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B TYR* 4.3 13.4 - - - +
384B TYR* 5.0 0.2 - - - -
401B LYS* 3.7 32.3 - - - +
402B PHE 3.2 12.1 - - - +
403B THR* 4.1 11.2 - - + -
411B PRO* 3.3 12.7 - - - +
412B GLN* 1.4 81.7 - - + +
414B PHE* 1.3 68.7 + - - +
415B TRP* 6.0 2.9 - - - +
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Residues in contact with PHE 414 (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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338B PHE* 3.7 18.8 - + + -
340B LEU* 3.4 25.4 - - + -
361B THR* 3.6 30.1 - - + -
362B VAL 3.3 12.8 - - - +
363B TYR* 4.2 7.6 - - - -
381B PHE* 3.9 13.2 - + + -
384B TYR* 3.6 30.7 - + - -
401B LYS* 3.6 5.2 - - - +
402B PHE* 2.7 74.3 + + + +
411B PRO* 4.3 8.3 - - + -
413B LYS* 1.3 76.6 - - - +
415B TRP* 1.3 73.3 + - - +
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Residues in contact with TRP 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU 3.4 1.4 - - - +
361B THR* 3.3 5.5 - - - -
362B VAL* 2.8 47.8 + - + +
363B TYR 3.8 14.0 + - - -
364B LYS* 3.9 4.3 - - - +
365B ALA* 3.4 42.5 + - + +
368B LEU* 3.7 34.8 - - + -
370B LEU* 3.7 25.1 - - + -
389B ALA* 3.9 7.9 - - + -
400B TRP 3.5 5.4 - - - -
401B LYS* 3.6 50.6 - - + +
413B LYS* 6.0 3.0 - - - +
414B PHE* 1.3 81.6 - - - +
416B GLY* 1.3 59.2 - - - +
417B LEU* 3.9 11.2 - - + -
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Residues in contact with GLY 416 (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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359B THR* 3.5 21.8 - - - -
360B LEU 3.5 5.8 - - - -
361B THR* 4.6 1.6 - - - -
399B GLY* 3.2 2.9 - - - -
400B TRP* 2.8 40.7 + - - -
402B PHE* 3.9 14.1 - - - -
414B PHE* 4.9 2.0 - - - -
415B TRP* 1.3 70.5 - - - +
417B LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 417 (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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331B ILE* 3.8 15.3 - - + -
332B THR* 3.7 30.5 - - + -
358B GLU 3.4 1.9 - - - +
359B THR* 3.4 2.4 - - - -
360B LEU* 2.9 42.1 + - + +
362B VAL* 4.0 15.3 - - + -
365B ALA* 4.7 0.9 - - + -
368B LEU* 4.4 14.1 - - + -
389B ALA* 5.9 0.2 - - + -
398B ILE* 3.5 22.9 - - + +
399B GLY* 4.8 1.6 - - - +
400B TRP 5.2 0.2 - - - +
415B TRP* 3.9 19.3 - - + -
416B GLY* 1.3 80.2 - - - +
418B THR* 1.3 63.3 + - - +
419B ARG 3.5 1.0 + - - -
422B LEU* 3.8 25.1 - - + +
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Residues in contact with THR 418 (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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357B HIS* 3.1 40.8 + - + +
358B GLU 3.4 6.4 + - - -
359B THR* 4.8 0.4 - - - +
397B HIS* 4.0 22.7 - - + +
398B ILE 2.9 23.1 + - - +
399B GLY* 4.2 0.2 - - - -
400B TRP* 4.4 7.1 - - - -
416B GLY 4.1 1.4 + - - -
417B LEU* 1.3 70.3 - - - +
419B ARG* 1.3 59.3 + - - +
420B SER* 3.2 19.0 + - - +
421B ALA* 2.9 34.4 + - + +
422B LEU* 3.8 6.4 + - - +
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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