Contacts of the strand formed by residues 443 - 448 (chain N) in PDB entry 5D4D
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 443 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400N VAL* 4.0 20.0 - - + -
401N TYR 3.5 31.2 - - - +
402N PRO* 3.7 9.4 - - + -
403N PHE* 3.2 9.3 - - - -
438N ASP* 2.9 45.9 + - + +
441N ARG* 3.8 21.5 - - + +
442N ASN* 1.3 78.0 - - - +
444N VAL* 1.3 67.6 + - - +
445N ARG* 3.6 14.1 + - - +
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Residues in contact with VAL 444 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401N TYR* 2.9 41.0 + - + +
403N PHE* 3.5 8.2 - - + -
407N VAL* 3.6 35.7 - - + -
409N VAL* 4.0 4.3 - - + -
421N LEU* 3.9 29.8 - - + +
422N ALA* 4.2 9.6 - - + -
435N VAL* 3.9 26.0 - - + -
436N GLU 4.0 2.2 - - - -
437N VAL* 4.3 8.7 - - + +
443N VAL* 1.3 72.6 - - - +
445N ARG* 1.3 59.5 + - - +
446N VAL* 4.6 4.7 - - + -
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Residues in contact with ARG 445 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202N VAL* 4.5 10.5 - - - -
204N LEU* 3.9 27.5 - - - +
396N VAL* 5.1 4.2 - - - +
398N ALA* 3.7 25.4 - - + -
399N ARG 3.5 7.6 - - - +
400N VAL* 4.3 15.1 - - + +
435N VAL* 3.9 1.9 - - - +
436N GLU* 2.8 76.5 + - - +
437N VAL 5.5 0.2 - - - -
438N ASP* 3.6 35.4 + - - +
441N ARG* 3.8 9.7 - - - +
443N VAL* 3.6 11.4 + - + +
444N VAL* 1.3 72.9 - - - +
446N VAL* 1.3 62.4 + - - +
447N VAL* 3.8 1.8 + - + +
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Residues in contact with VAL 446 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398N ALA* 3.1 5.3 - - - -
399N ARG* 2.9 34.3 + - - +
401N TYR* 4.0 28.7 - - + -
415N VAL* 3.8 21.5 - - + -
421N LEU* 4.1 17.7 - - + -
429N SER* 4.0 3.1 - - - +
431N VAL* 4.0 18.4 - - + -
433N GLY* 3.7 27.1 - - - -
434N ARG 3.7 2.5 - - - -
435N VAL* 4.5 7.9 - - + -
444N VAL* 4.6 2.7 - - + -
445N ARG* 1.3 74.8 - - - +
447N VAL* 1.3 60.9 + - - +
448N GLU* 3.6 1.6 + - - +
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Residues in contact with VAL 447 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163N TYR 4.0 21.1 - - - +
164N GLY* 4.7 6.1 - - - -
165N LYS 5.4 1.1 - - - +
166N GLN* 5.2 4.7 - - - +
396N VAL* 3.7 17.7 - - + -
397N LYS 3.5 11.0 - - - +
398N ALA* 3.6 9.9 - - + -
433N GLY* 3.0 4.9 - - - -
434N ARG* 2.9 44.1 + - + +
436N GLU* 3.8 34.3 - - + +
445N ARG* 4.4 2.9 - - + +
446N VAL* 1.3 71.6 - - - +
448N GLU* 1.3 67.3 + - - +
449N SER* 3.1 1.8 + - - -
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Residues in contact with GLU 448 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N GLU 4.5 1.0 - - - +
164N GLY* 3.2 22.3 - - - -
165N LYS 4.6 0.9 + - - -
397N LYS* 3.0 58.6 + - + +
398N ALA* 4.6 2.2 - - - -
399N ARG* 3.6 35.1 + - - -
431N VAL* 3.8 28.8 - - + +
432N TYR 3.7 6.1 - - - +
446N VAL 4.5 3.6 - - - +
447N VAL* 1.3 68.5 - - - +
449N SER* 1.3 58.0 + - - +
450N TYR* 5.8 2.0 - - - -
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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