Contacts of the strand formed by residues 402 - 412 (chain A) in PDB entry 4B92
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 VAL 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.7 15.5 - - + -
28A VAL* 5.2 2.0 - - + -
30A ILE* 4.3 10.3 - - + -
35A ILE* 3.9 17.5 - - + -
58A VAL* 3.5 31.0 - - + -
59A ILE 3.7 7.9 - - - +
61A GLY 4.0 0.4 - - - +
95A THR* 4.4 0.2 - - - +
394A ILE* 3.6 19.1 - - + -
400A ALA* 3.5 11.4 - - - -
401A ASP* 1.3 77.7 - - - +
403A VAL* 1.3 69.3 + - - +
438A VAL 4.3 0.2 - - - +
440A ILE* 2.8 45.2 + - + +
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Residues in contact with VAL 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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57A LEU 3.5 0.3 - - - +
58A VAL* 3.5 2.3 - - - -
59A ILE* 2.9 45.6 + - + +
61A GLY* 3.8 12.8 - - - +
93A GLY* 3.5 30.3 - - - +
95A THR* 4.1 7.9 - - + -
402A VAL* 1.3 80.6 - - - +
404A VAL* 1.3 70.5 + - - +
405A TRP* 3.4 16.2 + - + +
436A PRO* 3.7 25.4 - - + -
438A VAL 3.5 10.5 - - - +
439A THR* 4.1 8.3 - - + -
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Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.7 37.7 - - + -
51A ILE* 4.3 11.4 - - + -
52A ASP 5.3 1.3 - - - +
53A ALA* 4.2 10.5 - - + -
56A LYS* 3.9 28.3 - - + -
57A LEU 3.5 3.4 - - - +
58A VAL* 4.8 2.9 - - + -
402A VAL 4.4 0.2 + - - -
403A VAL* 1.3 71.6 - - - +
405A TRP* 1.3 58.0 + - - +
436A PRO* 3.7 1.9 - - - +
437A LEU* 2.9 39.2 + - + +
438A VAL* 2.9 34.7 + - + +
440A ILE* 5.3 1.1 - - + +
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Residues in contact with TRP 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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56A LYS* 3.4 5.1 - - - +
57A LEU* 2.7 68.8 + - + +
59A ILE* 4.2 28.3 - - + -
92A GLY 4.5 1.3 - - - -
93A GLY* 4.9 0.9 - - - -
355A MET* 3.7 20.4 - - + -
356A SER* 3.6 32.1 - - - -
359A TRP* 3.4 44.2 - + + -
373A PHE* 4.5 3.6 - + - -
403A VAL* 3.4 7.6 + - + -
404A VAL* 1.3 72.5 - - - +
406A ASP* 1.3 59.6 + - - +
407A PRO* 3.3 10.1 - - + +
434A GLY* 3.4 25.4 - - - -
435A VAL 3.8 4.5 - - - -
436A PRO* 3.4 37.0 - - + -
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Residues in contact with ASP 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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56A LYS* 2.8 32.2 + - - -
404A VAL 4.0 1.2 + - - -
405A TRP* 1.3 71.8 - - - +
407A PRO* 1.3 66.8 - - - +
408A GLU* 3.0 22.7 + - - +
409A ALA* 3.3 29.5 + - + +
434A GLY* 3.5 3.5 + - - -
435A VAL 2.8 38.4 + - - +
437A LEU* 3.6 25.4 - - + +
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Residues in contact with PRO 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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55A GLY 3.8 21.3 - - - +
56A LYS* 4.1 2.7 - - - -
57A LEU* 4.0 19.1 - - + -
359A TRP* 3.8 39.0 + - + +
364A VAL* 5.3 1.2 - - - +
405A TRP* 3.3 15.0 - - + +
406A ASP* 1.3 87.8 - - - +
408A GLU* 1.3 66.7 + - + +
433A HIS* 4.2 9.7 - - - +
434A GLY 4.5 1.8 - - - -
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Residues in contact with GLU 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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55A GLY* 3.7 18.4 - - - +
56A LYS* 4.1 9.4 + - - -
406A ASP* 3.0 12.7 + - - +
407A PRO* 1.3 85.8 - - + +
409A ALA* 1.3 72.4 + - - +
410A THR* 3.5 2.8 + - - +
433A HIS* 3.4 21.6 - - - -
434A GLY 4.7 0.2 - - - -
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Residues in contact with ALA 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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406A ASP* 3.3 28.7 + - + +
407A PRO 3.8 0.2 - - - -
408A GLU* 1.3 83.1 - - - +
410A THR* 1.3 61.7 + - - +
411A LYS 4.3 0.2 + - - -
432A CYS 3.7 0.3 - - - +
433A HIS* 3.5 0.5 - - - -
434A GLY* 3.1 25.6 + - - -
435A VAL* 4.4 14.4 - - + +
437A LEU* 5.3 1.3 - - + -
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Residues in contact with THR 410 (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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408A GLU 3.6 2.2 - - - +
409A ALA* 1.3 76.6 - - - +
411A LYS* 1.3 62.2 + - - +
431A ARG* 5.2 18.8 + - + +
432A CYS 3.2 10.8 - - - +
433A HIS* 3.3 41.5 - - + +
435A VAL* 5.3 0.2 - - - -
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Residues in contact with LYS 411 (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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91A VAL* 6.0 2.0 - - - +
352A GLN* 4.8 14.9 - - - +
356A SER* 5.7 4.5 - - - +
409A ALA 4.3 0.2 + - - -
410A THR* 1.3 74.8 - - - +
412A THR* 1.3 75.1 + - - +
413A ILE* 4.8 15.7 - - + +
414A SER 5.8 0.2 - - - +
417A THR* 4.7 18.4 + - - -
431A ARG* 4.2 0.3 - - - -
432A CYS* 3.1 32.1 + - + +
435A VAL* 3.9 27.3 - - + +
447A TYR* 5.6 3.6 + - - -
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Residues in contact with THR 412 (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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411A LYS* 1.3 84.0 + - - +
413A ILE* 1.3 66.3 + - - +
414A SER* 3.3 8.1 + - - -
417A THR* 4.9 2.6 + - - +
429A ASN* 3.7 37.9 - - - +
430A MET 3.6 3.1 - - - -
431A ARG* 4.3 17.7 + - - +
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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