Contacts of the strand formed by residues 404 - 407 (chain N) in PDB entry 2JA7
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 404 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216N GLU* 3.5 31.3 + - + +
217N ARG* 3.3 18.4 - - - +
218N SER* 4.0 18.4 - - - +
219N ALA 3.9 0.2 - - - +
398N ARG 4.3 22.0 + - - +
399N ASP* 4.8 8.5 + - + +
400N HIS 3.9 3.6 - - - +
401N PHE* 3.3 47.5 + - + +
402N GLY 4.4 0.2 - - - -
403N LYS* 1.3 82.9 - - + +
405N ARG* 1.3 76.4 + - - +
406N LEU* 5.4 1.6 - - - +
500N THR* 5.8 3.6 - - - +
518N HIS* 6.2 0.4 - - + -
631N GLY 3.7 2.9 - - - +
632N ARG* 4.7 3.3 - - - -
633N VAL* 5.3 2.4 + - - +
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Residues in contact with ARG 405 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217N ARG* 2.7 74.8 + - - +
219N ALA* 3.1 34.1 - - + +
220N GLY 5.8 0.2 + - - -
222N ILE* 4.7 6.7 - - - +
402N GLY 3.0 26.4 + - - -
404N LYS* 1.3 83.5 + - - +
406N LEU* 1.3 64.2 + - - +
407N ASP 3.3 2.2 + - - +
627N PHE* 4.4 18.8 - - - -
629N ASP* 3.5 28.8 + - - +
631N GLY* 3.0 35.4 - - - +
632N ARG* 3.1 29.5 - - - +
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Residues in contact with LEU 406 (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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214N ALA* 4.7 8.1 - - + -
216N GLU* 3.4 48.5 - - + +
401N PHE* 4.3 13.0 - - + -
404N LYS 5.4 0.7 - - - +
405N ARG* 1.3 72.4 - - - +
407N ASP* 1.3 68.1 + - - +
408N LEU* 3.2 8.7 + - - +
498N THR* 3.6 23.1 - - + +
522N VAL* 6.0 0.2 - - + -
539N LEU* 4.0 15.3 - - + -
545N ILE* 4.2 20.4 - - + +
631N GLY* 3.0 19.5 + - - +
633N VAL* 3.6 29.8 - - + -
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Residues in contact with ASP 407 (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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213N ILE 4.8 0.3 - - - +
214N ALA* 3.9 2.1 - - - -
215N GLN* 3.1 40.2 + - + +
217N ARG* 2.9 51.5 + - - +
405N ARG* 3.3 3.8 + - - +
406N LEU* 1.3 75.4 - - - +
408N LEU* 1.3 59.2 + - - +
411N PRO* 4.4 18.2 - - + +
412N LEU* 4.9 11.2 - - + +
476N ARG* 5.9 0.5 + - - -
630N ALA 4.7 4.0 - - - +
631N GLY* 5.6 1.8 - - - -
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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