Contacts of the strand formed by residues 425 - 432 (chain A) in PDB entry 3L2P
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A GLY* 1.3 79.5 - - - +
426A ARG* 1.3 68.3 + - - +
427A VAL* 3.3 5.7 + - + +
440A SER* 6.5 0.2 - - - -
446A VAL* 5.3 3.6 - - - +
450A LYS* 2.7 40.6 + - - +
473A GLU* 3.5 3.8 + - - +
474A VAL* 2.9 37.6 + - + +
487A PHE* 4.4 9.2 - - + -
490A LEU* 3.9 18.6 - - + +
10B T 3.5 46.0 + - + +
11B C 3.8 5.8 - - - +
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Residues in contact with ARG 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A PRO* 3.5 16.3 - - + +
397A MET 2.7 36.1 + - - +
398A LEU* 4.6 5.3 - - - +
425A GLU* 1.3 72.1 - - - +
427A VAL* 1.3 66.4 + - - +
428A GLN* 5.1 2.0 - - + +
440A SER* 3.6 20.8 - - - -
441A ARG* 3.7 25.6 + - + +
446A VAL* 4.8 0.2 - - - +
471A ASP* 2.5 42.5 + - - +
472A SER 3.5 8.5 - - - -
473A GLU* 3.4 17.8 + - - +
508A PHE* 3.5 13.7 - - - -
579A TYR* 3.6 0.2 + - - -
586A TRP* 3.7 8.8 - - - -
901A AMP 3.1 33.0 + - - +
11B C 3.3 15.9 + - - +
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Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLU* 3.3 13.8 + - + +
426A ARG* 1.3 83.1 - - - +
428A GLN* 1.3 61.5 + - - +
429A VAL* 3.8 9.0 + - + -
438A TYR* 4.0 31.9 - - + -
439A PHE 3.4 6.5 - - - +
446A VAL* 3.9 18.8 - - + -
451A VAL* 4.6 3.4 - - + -
471A ASP* 4.9 0.2 - - - -
472A SER* 2.7 52.6 + - - +
474A VAL* 3.8 20.6 - - + -
505A LEU* 4.6 7.9 - - + -
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Residues in contact with GLN 428 (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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393A PRO* 3.8 1.9 - - - +
394A VAL* 2.6 51.0 + - - +
396A PRO* 4.4 13.8 - - + +
426A ARG* 4.2 3.8 - - + +
427A VAL* 1.3 72.3 - - - +
429A VAL* 1.3 59.4 + - - +
430A HIS* 2.5 32.0 + - + +
437A SER 3.7 0.7 - - - +
438A TYR* 3.6 1.4 - - - -
439A PHE* 2.8 46.8 + - + +
440A SER 5.4 1.5 + - - +
443A LEU* 4.3 7.5 - - + +
469A ILE* 3.9 7.8 - - + +
470A LEU 3.4 14.6 - - - +
471A ASP* 4.6 9.0 + - - +
511A ILE* 4.6 8.2 - - + +
579A TYR* 5.2 0.6 + - - -
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 4.1 13.0 - - + -
428A GLN* 1.3 74.3 - - - +
430A HIS* 1.3 71.9 + - - +
431A LYS* 4.8 3.6 - - + +
436A PHE* 4.8 2.2 - - + -
437A SER 3.6 3.8 - - - +
438A TYR* 4.0 19.3 - - + -
458A ILE* 3.8 25.8 - - + -
468A MET* 3.8 0.9 - - + +
469A ILE* 3.2 4.9 - - - +
470A LEU* 2.9 49.0 + - + +
472A SER* 4.3 4.0 - - - +
505A LEU* 4.0 27.8 - - + -
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Residues in contact with HIS 430 (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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389A SER 4.3 2.0 - - - -
391A MET* 2.5 42.4 + - + +
392A THR 3.1 32.5 + - - -
394A VAL* 4.6 2.7 - - + -
428A GLN* 2.5 30.8 + - + -
429A VAL* 1.3 82.0 - - - +
431A LYS* 1.3 59.2 + - - +
436A PHE* 3.5 2.3 - - - -
437A SER* 2.8 38.4 + - - +
439A PHE* 3.4 23.6 - + - -
468A MET 3.5 4.3 - - - -
469A ILE* 3.2 26.0 - - + +
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Residues in contact with LYS 431 (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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390A LEU* 3.8 2.8 - - - +
391A MET* 4.0 1.3 - - - -
429A VAL* 4.9 3.6 - - + -
430A HIS* 1.3 76.2 - - - +
432A ASN* 1.3 62.8 + - - +
433A GLY 2.5 28.9 + - - +
434A ASP* 5.0 0.8 - - - +
435A HIS 3.3 7.2 - - - +
436A PHE* 3.6 39.9 - - + -
458A ILE* 4.0 15.7 - - + -
459A PRO* 4.5 13.9 - - - -
465A GLY 3.1 21.3 + - - +
466A HIS* 3.1 18.1 + - - +
467A SER* 3.2 5.0 - - - -
468A MET* 3.1 46.2 + - + +
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Residues in contact with ASN 432 (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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390A LEU* 3.3 29.9 - - + +
391A MET* 3.9 19.2 - - + +
431A LYS* 1.3 75.3 - - - +
433A GLY* 1.3 67.2 + - - +
434A ASP 3.0 0.3 + - - -
435A HIS* 2.8 42.0 + - + +
466A HIS 3.8 1.6 - - - -
467A SER* 4.2 6.8 - - - +
515A ASP* 5.6 0.5 - - - +
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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