Contacts of the strand formed by residues 398 - 402 (chain N) in PDB entry 4G7Z
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 ALA 398 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184N GLU* 3.7 6.6 - - - +
201N GLY* 4.8 2.0 - - - -
202N VAL* 3.3 24.2 + - + +
396N VAL* 3.4 25.0 + - + -
397N LYS* 1.3 77.9 - - - +
399N ARG* 1.3 75.3 + - - +
445N ARG* 4.5 11.2 - - + -
446N VAL 3.3 19.3 - - - +
447N VAL* 4.2 1.1 - - + +
448N GLU* 4.2 6.3 + - - +
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Residues in contact with ARG 399 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184N GLU* 5.1 5.6 + - - -
398N ALA* 1.3 80.7 + - - +
400N VAL* 1.3 63.6 + - - +
401N TYR* 3.4 36.2 + - + +
430N ASP* 4.9 4.8 - - - +
431N VAL* 3.2 33.6 - - + +
444N VAL 3.8 1.0 - - - +
445N ARG* 3.4 8.8 - - - +
446N VAL* 3.0 34.6 + - + +
448N GLU* 3.8 19.4 + - + +
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Residues in contact with VAL 400 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182N GLY* 5.0 7.2 - - - +
184N GLU* 3.8 23.8 - - - +
202N VAL* 3.8 31.6 - - + -
399N ARG* 1.3 73.7 - - - +
401N TYR* 1.3 67.2 + - - +
402N PRO* 3.5 11.2 - - + +
443N VAL* 4.0 21.1 - - + -
445N ARG* 4.0 10.3 - - + +
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Residues in contact with TYR 401 (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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399N ARG* 3.4 35.3 - - + +
400N VAL* 1.3 75.7 - - - +
402N PRO* 1.3 65.7 - - + +
421N LEU* 3.5 22.4 - - + -
427N VAL* 3.9 22.8 - - + +
428N LYS 3.6 11.4 - - - -
429N SER* 4.0 3.8 - - - -
430N ASP* 2.9 51.1 + - - +
431N VAL 4.1 0.7 + - - -
443N VAL* 3.9 3.0 - - - +
444N VAL* 2.6 55.3 + - + +
446N VAL* 3.7 17.3 - - + -
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Residues in contact with PRO 402 (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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400N VAL* 3.5 12.8 - - + +
401N TYR* 1.3 87.3 - - + +
403N PHE* 1.3 60.8 + - - +
404N GLU* 5.9 0.2 - - - -
423N ASP* 4.4 0.9 - - - +
427N VAL* 4.2 17.0 - - + +
442N ASN 3.7 15.0 - - - +
443N VAL* 4.2 5.6 - - + -
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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