Contacts of the strand formed by residues 399 - 409 (chain A) in PDB entry 2XNF
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 LEU 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A VAL* 4.0 14.4 - - + +
396A SER 4.7 0.7 - - - +
398A LYS* 1.3 78.6 - - - +
400A LEU* 1.3 65.8 + - - +
401A ALA 3.3 0.2 + - - -
432A TYR* 3.0 3.6 - - - -
433A VAL* 2.7 60.8 + - + +
435A HIS* 3.5 55.2 - - + +
437A GLU 5.7 2.9 - - - +
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Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A VAL* 4.8 4.2 - - + +
398A LYS 4.0 1.0 + - - -
399A LEU* 1.3 73.3 - - - +
401A ALA* 1.3 64.9 + - - +
402A TRP 3.9 10.8 - - - +
403A SER* 3.6 23.6 - - - +
430A GLN* 5.0 12.8 - - + +
431A VAL 4.0 1.3 - - - +
432A TYR* 3.5 35.9 - - + +
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A LEU* 4.1 2.5 - - + +
400A LEU* 1.3 79.0 - - - +
402A TRP* 1.3 60.3 + - + +
431A VAL* 2.9 9.8 + - + +
433A VAL* 3.6 35.0 - - + -
439A LEU* 5.5 3.1 - - + +
441A THR* 2.7 36.4 + - + +
444A TRP* 6.4 0.2 - - + -
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Residues in contact with TRP 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A LEU* 3.9 2.7 - - - +
401A ALA* 1.3 79.9 - - + +
403A SER* 1.3 71.2 + - - +
404A GLY* 3.5 37.2 - - - -
405A VAL 3.9 8.1 - - - -
406A LEU* 4.0 8.1 - - + -
429A CYS* 4.1 2.2 - - - -
431A VAL* 2.7 65.7 + - + +
441A THR* 3.6 38.7 + - + -
444A TRP* 3.6 24.0 + + + +
445A PRO 3.1 27.4 + - - -
446A GLN* 3.8 10.8 - - - +
448A LEU* 3.7 31.2 - - + -
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Residues in contact with SER 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A LEU* 3.6 18.0 - - - +
402A TRP* 1.3 91.1 + - - +
404A GLY* 1.3 58.0 + - - +
429A CYS 3.4 11.4 - - - -
430A GLN* 4.0 14.0 + - - +
446A GLN* 5.9 1.9 - - - +
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Residues in contact with GLY 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A TRP* 3.5 26.2 - - - -
403A SER* 1.3 75.3 - - - +
405A VAL* 1.3 67.0 + - - -
428A PRO* 3.7 1.2 - - - +
429A CYS* 2.8 35.2 + - - +
446A GLN* 4.0 5.8 - - - -
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A TRP* 4.0 0.9 - - - -
404A GLY* 1.3 78.7 - - - -
406A LEU* 1.3 68.3 + - - +
426A SER* 3.7 28.3 - - - -
427A LEU 3.6 14.6 - - - +
428A PRO* 4.3 14.1 - - + -
446A GLN* 2.9 25.6 + - + +
447A LYS* 3.2 33.8 - - + -
448A LEU 3.4 2.4 + - - -
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A TRP* 4.0 3.6 - - + -
405A VAL* 1.3 78.0 - - - +
407A GLU* 1.3 62.5 + - - +
408A TRP* 4.0 2.0 + - + -
425A ARG 3.6 0.7 - - - +
426A SER* 3.1 3.1 - - - -
427A LEU* 2.8 37.6 + - + +
429A CYS* 3.4 22.7 - - - -
448A LEU* 3.6 41.7 - - + +
450A MET* 3.7 30.5 - - + -
473A PHE* 3.6 26.9 - - + -
475A PHE* 3.8 19.5 - - + -
498A VAL* 5.1 3.6 - - + -
513A LEU* 4.1 2.7 - - + -
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Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A VAL 4.2 0.4 + - - -
406A LEU* 1.3 73.4 - - - +
408A TRP* 1.3 60.4 + - - +
409A GLN* 5.4 0.2 - - - +
424A THR* 3.6 28.5 - - + +
425A ARG 3.1 3.4 - - - +
426A SER* 3.6 26.9 - - - -
447A LYS* 2.8 46.0 + - + +
448A LEU 3.0 13.1 + - - +
449A ILE* 3.6 6.4 - - + +
450A MET* 3.0 25.3 + - - +
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Residues in contact with TRP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A LEU* 4.5 2.7 - - + -
407A GLU* 1.3 74.7 - - - +
409A GLN* 1.3 65.9 + - - +
410A GLU* 4.2 18.3 + - + -
423A LEU 4.2 0.9 - - - +
424A THR* 3.5 3.8 - - - -
425A ARG* 2.8 77.6 + - + +
426A SER 4.8 0.6 + - - -
427A LEU* 4.3 20.6 - - + +
450A MET* 3.2 34.5 - - + +
452A LEU* 3.8 20.9 - - + -
482A SER* 5.0 18.8 - - - -
485A GLY 6.1 0.7 - - - -
486A LEU* 4.2 30.3 - - + +
489A ILE* 4.7 18.8 - - + -
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Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A GLU 5.4 0.2 - - - +
408A TRP* 1.3 78.7 - - - +
410A GLU* 1.3 60.9 + - - +
411A LYS 4.0 15.4 + - - +
412A PRO* 4.4 12.3 + - - +
421A THR* 3.5 30.5 + - - +
422A LYS* 4.8 1.8 - - - +
423A LEU 4.4 4.7 + - - +
424A THR* 3.6 28.9 + - + +
449A ILE* 4.2 19.9 - - + +
450A MET 2.9 9.7 + - - +
451A GLN* 2.8 30.5 - - + +
452A LEU* 3.3 15.6 + - - +
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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