Contacts of the strand formed by residues 31 - 39 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H VAL* 3.4 5.3 - - - +
28H GLU* 3.1 30.6 + - + +
29H GLY* 3.1 11.8 - - - +
30H GLY* 1.3 84.2 - - - +
32H ILE* 1.3 68.9 + - - +
33H LYS* 3.2 1.9 + - - +
508H GLY* 3.3 28.5 - - - +
509H THR 3.2 3.8 - - - +
510H PRO* 4.1 9.0 - - + -
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Residues in contact with ILE 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H VAL* 4.1 15.0 - - + -
26H GLU 3.5 4.9 - - - -
27H VAL* 4.5 3.8 - - + +
31H LYS* 1.3 74.3 - - - +
33H LYS* 1.3 56.0 + - - +
34H ASN 3.4 25.1 - - - +
506H LEU* 3.1 40.8 - - + +
507H ILE* 3.7 5.3 - - - +
508H GLY* 2.8 24.4 + - - -
509H THR* 2.8 40.2 + - - +
511H ILE* 3.5 25.6 - - + -
520H ILE* 3.7 20.2 - - + -
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Residues in contact with LYS 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H GLU* 2.7 50.2 + - + +
27H VAL 4.8 0.2 - - - -
28H GLU* 3.6 47.8 + - + +
31H LYS* 3.2 1.8 + - + +
32H ILE* 1.3 72.4 - - - +
34H ASN* 1.3 61.0 + - + +
507H ILE* 3.9 16.9 - - - +
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Residues in contact with ASN 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H VAL* 3.5 0.7 - - - -
26H GLU* 3.2 36.7 + - - +
32H ILE* 3.4 8.4 - - - +
33H LYS* 1.3 82.4 + - + +
35H ALA* 1.3 83.8 + - - +
36H TRP* 3.7 28.4 - - + -
493H ARG* 2.8 29.6 + - - +
499H LEU* 4.2 7.8 - - - +
507H ILE* 4.0 5.4 - - - -
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Residues in contact with ALA 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLU 3.6 2.0 - - - -
25H VAL* 4.0 5.4 - - + -
32H ILE* 4.3 0.7 - - + -
34H ASN* 1.3 94.2 + - - +
36H TRP* 1.3 61.9 + - - +
493H ARG* 2.7 31.5 + - - -
499H LEU* 4.8 0.2 - - - +
503H GLU* 3.6 22.2 - - - +
506H LEU* 3.8 39.3 - - + -
507H ILE* 4.0 3.6 - - + +
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Residues in contact with TRP 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H LYS* 4.6 11.7 - - + -
22H ARG 4.1 0.2 - - - +
23H ILE* 3.8 8.3 - - - +
24H GLU* 3.0 63.0 + - + +
25H VAL* 4.2 1.8 - - - -
26H GLU* 3.7 39.3 - - + -
34H ASN* 3.7 24.5 - - + -
35H ALA* 1.3 84.4 - - - +
37H SER* 1.3 61.7 + - - +
38H MET* 3.8 9.0 + - + +
349H HIS* 3.8 27.5 + + + -
354H TYR* 4.0 22.7 - + + -
493H ARG* 3.1 26.5 - - - +
503H GLU* 3.5 5.4 - - - -
506H LEU* 6.2 0.7 - - - -
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Residues in contact with SER 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H LEU* 3.7 14.0 - - - +
22H ARG 4.2 2.2 - - - -
23H ILE* 4.3 8.5 - - - +
36H TRP* 1.3 70.9 - - - +
38H MET* 1.3 61.2 + - - +
39H SER* 4.0 0.6 + - - -
354H TYR* 3.4 16.3 - - - -
355H SER* 3.9 9.7 + - - -
490H LEU* 2.8 33.5 + - - +
491H GLY 4.5 0.4 - - - -
492H PRO* 4.7 1.0 - - - +
502H VAL* 3.7 25.4 - - - +
503H GLU* 2.9 17.3 + - - +
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Residues in contact with MET 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LEU* 3.4 4.6 - - - +
22H ARG* 2.7 62.0 + - + +
24H GLU* 3.4 34.3 - - - +
36H TRP* 4.1 7.6 - - + +
37H SER* 1.3 74.8 + - - +
39H SER* 1.3 61.2 - - - +
40H THR* 3.7 4.5 - - + +
327H TRP* 4.6 1.1 - - + -
348H PHE* 3.6 44.6 - - + -
349H HIS* 3.9 16.8 - - - +
354H TYR* 3.4 35.0 - - + +
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Residues in contact with SER 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H HIS 3.7 5.4 - - - -
21H LEU* 4.1 8.5 - - - +
38H MET* 1.3 71.1 - - - +
40H THR* 1.3 57.8 + - - +
41H LEU 3.8 1.1 - - - -
327H TRP* 3.6 5.7 - - - -
355H SER* 3.3 17.2 + - - -
356H TRP* 3.3 26.3 + - - -
357H MET* 3.4 27.7 - - - +
490H LEU 4.3 3.6 + - - -
531H ILE* 3.7 18.0 - - - +
535H VAL* 3.7 17.0 - - - -
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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