Contacts of the strand formed by residues 31 - 39 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D VAL* 3.4 5.7 - - - +
28D GLU* 3.1 30.1 + - + +
29D GLY 3.1 11.8 - - - +
30D GLY* 1.3 84.5 - - - +
32D ILE* 1.3 69.8 + - - +
33D LYS* 3.2 1.7 + - - +
508D GLY* 3.3 28.9 - - - +
509D THR 3.2 3.8 - - - +
510D PRO* 4.1 9.0 - - + -
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 4.1 14.6 - - + -
26D GLU 3.5 5.4 - - - +
27D VAL* 4.5 3.6 - - + -
31D LYS* 1.3 72.9 - - - +
33D LYS* 1.3 56.4 + - - +
34D ASN 3.4 24.7 - - - +
506D LEU* 3.1 39.7 - - + +
507D ILE* 3.7 5.8 - - - +
508D GLY* 2.8 24.3 + - - -
509D THR* 2.8 40.9 + - - +
511D ILE* 3.5 26.2 - - + +
520D ILE* 3.7 20.9 - - + -
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Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D GLU* 2.7 50.0 + - + +
27D VAL 4.8 0.2 - - - +
28D GLU* 3.6 49.1 + - + +
31D LYS 3.2 0.9 + - - +
32D ILE* 1.3 72.6 - - - +
34D ASN* 1.3 61.8 + - + +
507D ILE* 3.9 17.1 - - - +
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Residues in contact with ASN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 3.5 0.7 - - - -
26D GLU* 3.2 35.7 + - - +
32D ILE* 3.4 9.1 - - - +
33D LYS* 1.3 82.8 - - + +
35D ALA* 1.3 83.4 + - - +
36D TRP* 3.7 29.5 - - + -
493D ARG* 2.8 29.4 + - - +
499D LEU* 4.2 8.0 - - - +
507D ILE* 4.0 6.2 - - - +
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Residues in contact with ALA 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLU 3.6 2.5 - - - -
25D VAL* 4.0 4.5 - - + -
34D ASN* 1.3 95.3 + - - +
36D TRP* 1.3 63.4 + - - +
493D ARG* 2.7 31.0 + - - -
503D GLU* 3.6 23.3 - - + +
506D LEU* 3.8 39.9 - - + -
507D ILE* 4.0 3.8 - - + +
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Residues in contact with TRP 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LYS* 4.6 11.9 - - + -
23D ILE* 3.8 7.7 - - - +
24D GLU* 3.0 62.8 + - + +
25D VAL* 4.2 2.5 - - - -
26D GLU* 3.7 38.4 - - + -
34D ASN* 3.7 24.2 - - + -
35D ALA* 1.3 83.6 - - - +
37D SER* 1.3 61.4 + - - +
38D MET* 3.8 8.7 + - + +
349D HIS* 3.8 27.4 + + + -
354D TYR* 4.0 22.7 - + + -
493D ARG* 3.1 26.0 - - - +
503D GLU* 3.5 5.8 - - - -
506D LEU* 6.2 0.7 - - - -
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Residues in contact with SER 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 3.7 14.2 - - - +
22D ARG 4.2 2.0 - - - -
23D ILE* 4.3 8.2 - - - +
36D TRP* 1.3 71.7 - - - +
38D MET* 1.3 60.5 + - - +
354D TYR* 3.4 17.2 - - - -
355D SER* 3.9 9.4 + - - -
490D LEU* 2.8 33.1 + - - +
491D GLY 4.5 0.4 - - - -
492D PRO* 4.7 1.0 - - - +
502D VAL* 3.7 25.3 - - - +
503D GLU* 2.9 16.4 + - - -
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Residues in contact with MET 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 3.4 5.0 - - - +
22D ARG* 2.7 62.4 + - + +
24D GLU* 3.4 33.7 - - - +
36D TRP* 4.1 8.3 - - + +
37D SER* 1.3 75.1 + - - +
39D SER* 1.3 60.8 - - - +
40D THR* 3.7 4.5 - - + +
327D TRP* 4.6 0.9 - - + -
348D PHE* 3.6 44.6 - - + -
349D HIS* 3.9 17.5 - - + +
354D TYR* 3.4 34.3 - - + +
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Residues in contact with SER 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D HIS 3.7 5.6 - - - -
21D LEU* 4.1 8.7 - - - +
37D SER* 4.9 0.2 + - - -
38D MET* 1.3 69.7 - - - +
40D THR* 1.3 60.1 + - - +
41D LEU 3.8 1.3 - - - -
327D TRP* 3.6 5.7 - - - -
354D TYR 4.2 0.2 + - - -
355D SER* 3.3 17.9 + - - -
356D TRP* 3.3 26.1 + - - -
357D MET* 3.4 27.5 - - - +
490D LEU 4.3 3.5 + - - -
531D ILE* 3.7 18.2 - - - +
535D VAL* 3.7 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