Contacts of the strand formed by residues 31 - 39 (chain J) in PDB entry 2FRV
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 31 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344F LYS* 2.8 35.3 - - - +
27J VAL* 3.4 5.0 - - - +
28J GLU* 3.1 30.1 + - + +
29J GLY 3.1 12.9 - - - +
30J GLY* 1.3 84.2 - - - +
32J ILE* 1.3 69.7 + - - +
33J LYS* 3.2 2.3 + - + +
508J GLY* 3.3 28.7 - - - +
509J THR 3.2 4.0 - - - +
510J PRO* 4.1 9.2 - - + -
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Residues in contact with ILE 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J VAL* 4.1 14.6 - - + -
26J GLU 3.5 4.7 - - - -
27J VAL* 4.5 3.1 - - + -
31J LYS* 1.3 74.2 - - - +
33J LYS* 1.3 56.7 + - - +
34J ASN 3.4 24.9 - - - +
506J LEU* 3.1 40.8 - - + +
507J ILE* 3.7 5.7 - - - +
508J GLY* 2.8 24.4 + - - -
509J THR* 2.8 39.4 + - + +
511J ILE* 3.5 25.8 - - + -
520J ILE* 3.7 21.1 - - + -
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Residues in contact with LYS 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J GLU* 2.7 50.5 + - + +
27J VAL 4.8 0.2 - - - -
28J GLU* 3.6 47.6 - - + +
31J LYS* 3.2 1.1 + - + +
32J ILE* 1.3 73.2 - - - +
34J ASN* 1.3 61.6 + - + +
507J ILE* 3.9 17.5 - - - +
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Residues in contact with ASN 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J VAL* 3.5 0.9 - - - -
26J GLU* 3.2 35.6 + - - +
32J ILE* 3.4 9.3 - - - +
33J LYS* 1.3 82.9 + - + +
35J ALA* 1.3 82.7 + - - +
36J TRP* 3.7 28.2 - - + -
493J ARG* 2.8 28.0 + - - +
499J LEU* 4.2 8.7 - - - +
507J ILE* 4.0 6.2 - - - +
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Residues in contact with ALA 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J GLU 3.6 2.5 - - - -
25J VAL* 4.0 5.4 - - + -
34J ASN* 1.3 94.0 + - - +
36J TRP* 1.3 63.2 + - - +
493J ARG* 2.7 30.8 + - - -
503J GLU* 3.6 22.7 - - - +
506J LEU* 3.8 39.3 - - + -
507J ILE* 4.0 4.6 - - + +
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Residues in contact with TRP 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J LYS* 4.6 12.3 - - + -
22J ARG 4.1 0.2 - - - +
23J ILE* 3.8 8.2 - - - +
24J GLU* 3.0 63.1 + - + +
25J VAL* 4.2 2.0 - - - -
26J GLU* 3.7 39.3 - - + -
34J ASN* 3.7 25.1 - - + -
35J ALA* 1.3 84.5 - - - +
37J SER* 1.3 61.5 + - - +
38J MET* 3.8 8.2 + - + +
349J HIS* 3.8 28.2 + + + -
354J TYR* 4.0 22.7 - + + -
493J ARG* 3.1 25.8 - - - +
503J GLU* 3.5 6.1 - - - -
506J LEU* 6.2 0.4 - - - -
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Residues in contact with SER 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J LEU* 3.7 14.0 - - - +
22J ARG 4.2 2.0 - - - -
23J ILE* 4.3 8.6 - - - +
36J TRP* 1.3 70.5 - - - +
38J MET* 1.3 60.5 + - - +
39J SER 4.0 0.2 - - - -
354J TYR* 3.4 16.6 - - - -
355J SER* 3.9 10.0 + - - -
490J LEU* 2.8 32.3 + - - +
491J GLY 4.5 0.2 - - - -
492J PRO* 4.7 1.2 - - - +
502J VAL* 3.7 26.6 - - - +
503J GLU* 2.9 17.0 + - - +
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Residues in contact with MET 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J LEU* 3.4 5.4 - - - +
22J ARG* 2.7 62.1 + - + +
24J GLU* 3.4 33.9 - - - +
36J TRP* 4.1 8.7 - - + +
37J SER* 1.3 75.9 + - - +
39J SER* 1.3 59.7 + - - +
40J THR* 3.7 3.5 - - + +
327J TRP* 4.6 1.3 - - + -
348J PHE* 3.6 44.4 - - + -
349J HIS* 3.9 16.8 - - - +
354J TYR* 3.4 34.1 - - + +
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Residues in contact with SER 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J HIS 3.7 5.4 - - - -
21J LEU* 4.1 9.0 - - - +
38J MET* 1.3 69.1 - - - +
40J THR* 1.3 59.2 + - - +
41J LEU 3.8 1.6 - - - -
327J TRP* 3.6 5.4 - - - -
355J SER* 3.3 17.9 + - - -
356J TRP* 3.3 26.7 + - - +
357J MET* 3.4 26.7 - - - +
490J LEU 4.3 3.6 + - - -
531J ILE* 3.7 18.7 - - - +
535J VAL* 3.7 17.3 - - - -
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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