Contacts of the strand formed by residues 21 - 28 (chain L) 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 LEU 21 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12L ASP* 4.4 2.1 - - - -
13L PRO* 4.0 6.9 - - - +
14L ILE* 3.3 28.5 + - + +
17L ILE* 3.5 23.2 - - + +
19L GLY 3.6 3.8 + - - -
20L HIS* 1.3 72.8 - - - +
22L ARG* 1.3 66.6 + - - +
23L ILE* 4.1 18.6 - - + -
37L SER* 3.7 20.6 - - - +
38L MET 3.4 25.1 - - - +
39L SER* 4.1 9.4 - - - +
40L THR* 5.1 1.6 - - - -
490L LEU* 3.8 23.6 - - + -
524L VAL* 4.1 15.3 - - + -
529L PRO* 4.6 0.2 - - + -
531L ILE* 3.7 14.1 - - + -
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Residues in contact with ARG 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G GLU 3.5 13.3 + - - -
196G ALA* 3.3 27.3 + - - +
10L VAL* 3.8 12.9 - - + +
11L VAL 3.5 4.5 - - - +
12L ASP* 3.1 40.7 + - + +
21L LEU* 1.3 76.1 - - - +
23L ILE* 1.3 63.8 + - - +
24L GLU* 2.7 34.4 + - + -
37L SER 4.0 0.2 - - - -
38L MET* 2.7 57.8 + - + +
40L THR* 4.1 3.8 - - + -
348L PHE* 3.5 34.0 - - - -
88S GLY 4.1 13.1 + - - -
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Residues in contact with ILE 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ILE 3.8 0.7 - - - +
10L VAL* 3.2 4.0 - - - +
11L VAL* 2.6 41.3 + - + +
14L ILE* 3.4 31.9 - - + -
21L LEU* 4.1 15.0 - - + -
22L ARG* 1.3 74.7 - - - +
24L GLU* 1.3 65.1 + - - +
25L VAL* 3.7 24.5 - - + -
36L TRP 3.8 4.0 - - - +
37L SER* 4.3 20.0 - - - +
502L VAL* 5.1 4.5 - - + -
506L LEU* 3.9 16.8 - - + -
520L ILE* 4.0 13.0 - - + +
524L VAL* 3.7 21.3 - - + -
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Residues in contact with GLU 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G ALA* 4.7 2.8 - - - +
8L LYS* 4.6 13.0 - - + +
9L ILE 3.4 5.2 - - - +
10L VAL* 4.2 11.6 - - + +
22L ARG* 2.7 36.6 + - - +
23L ILE* 1.3 77.8 - - - +
25L VAL* 1.3 65.7 - - - +
36L TRP* 3.0 45.7 + - + +
38L MET* 3.4 22.6 - - - +
348L PHE* 4.8 1.0 - - - -
349L HIS* 2.6 32.5 + - - -
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Residues in contact with VAL 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L LYS* 2.9 13.1 - - - +
9L ILE* 2.8 63.7 + - + +
23L ILE* 3.7 20.6 - - + -
24L GLU* 1.3 79.6 - - - +
26L GLU* 1.3 58.3 + - - +
27L VAL* 3.8 14.8 - - + -
32L ILE* 4.1 13.9 - - + -
34L ASN 3.5 8.5 - - - +
35L ALA* 4.0 5.8 - - + -
36L TRP* 4.2 2.5 - - - -
506L LEU* 4.0 17.3 - - + -
520L ILE* 3.8 17.7 - - + -
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Residues in contact with GLU 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ASN 3.3 7.9 - - - +
8L LYS* 3.1 31.1 + - - +
25L VAL* 1.3 73.1 - - - +
27L VAL* 1.3 58.3 + - - +
32L ILE* 3.5 3.6 - - - -
33L LYS* 2.7 71.8 + - + +
34L ASN* 3.2 19.7 + - + +
36L TRP* 3.7 20.9 - - + -
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Residues in contact with VAL 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ASN 2.7 31.0 + - - +
9L ILE* 3.8 31.4 - - + -
25L VAL* 3.8 14.6 - - + -
26L GLU* 1.3 81.4 - - - +
28L GLU* 1.3 66.7 + - - +
30L GLY* 3.8 13.5 - - - +
31L LYS 3.4 24.0 - - - +
32L ILE* 4.5 6.5 - - + -
33L LYS* 4.8 0.7 - - - +
511L ILE* 4.5 13.7 - - + -
514L PRO* 6.2 2.9 - - + -
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Residues in contact with GLU 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L VAL* 1.3 76.4 - - - +
29L GLY* 1.3 65.6 + - - +
31L LYS* 3.1 20.9 + - + +
33L LYS* 3.6 41.0 - - + +
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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