Contacts of the strand formed by residues 425 - 430 (chain B) in PDB entry 2N5T
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 GLU 425 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B LYS* 3.8 10.6 + - - +
386B LEU 4.5 3.2 + - - -
387B ARG* 3.4 37.8 + - + +
388B ILE 2.9 25.3 + - - +
423B SER 3.6 12.6 - - - +
424B ILE* 1.3 77.9 - - - +
426B ILE* 1.3 62.3 + - - +
447B ASP* 3.2 35.5 - - + +
448B PHE* 4.0 12.5 - - + -
498B TRP* 4.6 7.9 + - - -
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Residues in contact with ILE 426 (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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388B ILE* 3.3 16.6 - - + +
390B PHE* 4.1 16.6 - - + -
399B VAL* 6.4 0.2 - - + -
403B ARG* 3.2 40.6 - - - +
406B ILE* 3.5 45.5 - - + -
410B LYS* 5.0 4.9 - - - +
424B ILE* 3.9 15.9 - - + +
425B GLU* 1.3 80.5 - - - +
427B GLY* 1.3 57.0 + - - +
446B VAL* 3.6 7.5 - - + -
447B ASP* 2.6 39.3 + - - +
448B PHE* 3.6 3.6 - - - -
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Residues in contact with GLY 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE 2.8 9.9 + - - +
389B MET* 3.4 8.7 - - - -
390B PHE* 3.3 22.0 + - - -
426B ILE* 1.3 75.3 - - - +
428B VAL* 1.3 70.6 + - - +
446B VAL* 3.9 4.9 - - - -
448B PHE* 3.2 28.1 - - - -
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Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B MET* 3.8 6.4 - - - +
390B PHE* 3.7 12.8 - - + -
393B ILE* 3.8 14.8 - - + -
399B VAL* 3.7 22.0 - - + -
426B ILE* 6.0 0.2 - - + -
427B GLY* 1.3 81.3 - - - +
429B MET* 1.3 71.7 + - - +
430B VAL* 3.5 1.5 + - + -
442B LEU* 4.8 11.4 - - + -
446B VAL* 3.6 22.7 - - + -
448B PHE* 3.2 3.8 + - - -
449B PHE* 3.3 34.2 - - + -
450B SER 3.2 20.1 + - - -
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Residues in contact with MET 429 (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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332B ARG* 3.4 29.2 - - - +
389B MET* 3.4 29.6 - - + +
390B PHE 2.7 22.3 + - - +
391B PRO* 3.7 11.2 - - + -
392B MET 4.3 0.9 - - - +
393B ILE* 4.0 14.9 + - - +
428B VAL* 1.3 80.4 - - - +
430B VAL* 1.3 59.3 + - - +
431B GLU* 3.3 23.5 + - + +
435B ALA* 4.5 2.4 - - - +
450B SER* 3.2 10.3 - - - +
452B GLY* 3.1 42.2 - - - +
502B CYS* 3.7 19.7 - - - -
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Residues in contact with VAL 430 (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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428B VAL* 4.5 1.1 - - + -
429B MET* 1.3 73.1 - - - +
431B GLU* 1.3 58.0 + - - +
432B THR 4.3 0.4 - - - +
435B ALA* 3.7 11.0 - - + +
436B ALA* 3.6 27.6 - - + +
439B ALA* 5.4 0.4 - - + -
442B LEU* 5.3 0.2 - - + -
449B PHE* 3.0 50.9 - - + -
450B SER 2.8 11.0 + - - +
451B ILE* 3.2 16.2 - - + +
452B GLY 2.9 18.1 + - - -
456B LEU* 4.5 2.5 - - + +
488B VAL* 3.5 34.5 - - + -
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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