Contacts of the strand formed by residues 29 - 33 (chain v) in PDB entry 6FF7
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 GLU 29 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19v HIS* 3.4 4.9 - - - +
20v GLY 2.9 36.4 + - - +
22v PHE* 4.9 15.3 - - + +
23v SER* 5.5 5.8 - - - +
27v GLN 4.3 0.4 + - - +
28v GLN* 1.3 74.4 - - - +
30v ILE* 1.3 64.0 + - - +
31v VAL 4.2 0.3 + - - -
40v LEU* 6.2 2.0 - - + -
41v LEU 3.6 12.6 - - - +
42v ARG* 5.1 6.5 - - + +
43v PRO 5.6 0.7 - - - -
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Residues in contact with ILE 30 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18v ILE 3.4 9.0 - - - +
19v HIS* 4.5 3.8 - - + +
29v GLU* 1.3 75.5 - - - +
31v VAL* 1.3 61.7 + - - +
32v VAL* 4.1 2.9 - - + +
40v LEU* 3.4 5.4 - - - +
41v LEU* 2.9 49.3 + - + +
43v PRO 5.8 0.4 - - - -
340v CYS* 5.6 6.3 - - + -
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Residues in contact with VAL 31 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17v ALA* 3.6 1.9 - - - -
18v ILE* 2.9 41.9 + - + +
19v HIS* 5.0 0.2 - - - +
22v PHE* 6.2 3.6 - - + -
29v GLU 4.2 0.6 + - - -
30v ILE* 1.3 74.0 - - - +
32v VAL* 1.3 60.8 - - - +
39v GLU 3.4 9.0 - - - +
40v LEU* 4.6 3.8 - - + +
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Residues in contact with VAL 32 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14v ILE* 5.0 9.6 - - + -
16v PHE 3.5 9.4 - - - +
17v ALA* 4.3 9.6 - - + +
30v ILE* 4.1 3.7 - - + -
31v VAL* 1.3 74.9 - - - +
33v SER* 1.3 63.4 + - - +
34v ARG 4.2 0.2 - - - -
38v LEU* 3.7 3.6 - - - +
39v GLU* 2.9 39.8 + - + +
41v LEU* 5.8 2.4 - - + +
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Residues in contact with SER 33 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14v ILE* 3.6 5.4 - - - -
15v SER* 3.2 24.8 + - - -
16v PHE* 2.9 26.2 + - - +
32v VAL* 1.3 74.7 - - - +
34v ARG* 1.3 58.7 + - - +
35v GLY* 3.1 6.6 + - - -
37v ILE 3.4 6.1 - - - -
38v LEU* 4.6 3.8 - - - +
62v ILE* 4.1 26.9 - - - -
65v LEU* 4.9 8.3 - - - -
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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