Contacts of the strand formed by residues 82 - 87 (chain D) in PDB entry 3FFC
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 SER 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D CYS 3.4 6.7 - - - -
24D THR* 3.6 20.2 - - - -
25D TYR* 3.9 3.3 - - - -
75D ASN 3.4 3.1 + - - +
76D PHE* 3.4 2.8 - - - -
77D GLN* 2.8 60.5 + - - +
80D ARG* 4.3 6.2 - - - +
81D LYS* 1.3 77.5 - - - +
83D ALA* 1.3 60.6 + - - +
84D ASN* 3.8 14.0 + - - -
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Residues in contact with ALA 83 (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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23D CYS* 2.9 15.5 + - - +
25D TYR* 4.4 1.3 - - + -
39D LEU* 3.7 33.0 - - + -
41D TRP* 3.0 26.1 + - - +
74D LEU* 3.6 17.9 - - + -
75D ASN 3.7 4.5 - - - -
76D PHE* 4.0 15.9 - - + +
82D SER* 1.3 74.3 - - - +
84D ASN* 1.3 62.7 + - - +
100D CYS* 5.1 0.2 - - - -
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Residues in contact with ASN 84 (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 THR* 3.4 23.1 - - + +
21D LEU 3.3 8.5 - - - +
22D ASP* 3.0 32.4 + - - +
23D CYS 3.2 21.3 + - - +
24D THR* 5.5 0.2 - - - +
74D LEU* 3.3 4.6 - - - +
75D ASN* 2.8 48.9 + - + +
82D SER* 4.0 13.7 + - - -
83D ALA* 1.3 72.6 - - - +
85D LEU* 1.3 59.6 + - - +
86D VAL 3.8 0.2 + - - -
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Residues in contact with LEU 85 (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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19D VAL 3.6 0.9 - - - +
20D THR* 3.4 5.2 - - - -
21D LEU* 2.9 37.3 + - + +
41D TRP* 3.4 40.0 - - + +
53D VAL* 4.6 2.5 - - + -
54D ILE* 3.9 25.4 - - + -
72D TYR* 4.0 24.5 - - + -
73D SER 3.6 9.6 - - - +
74D LEU* 4.6 0.2 - - - -
84D ASN* 1.3 71.9 - - - +
86D VAL* 1.3 66.7 + - - +
87D ILE* 3.9 21.6 + - + -
98D TYR* 3.7 30.7 - - + -
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Residues in contact with VAL 86 (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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18D ALA* 5.5 4.7 - - + -
19D VAL 3.3 10.8 - - - +
20D THR* 4.1 19.7 - - + +
71D ARG 3.2 6.2 - - - +
72D TYR* 3.6 0.3 - - - -
73D SER* 2.6 52.7 + - - +
75D ASN* 4.7 17.0 - - + +
85D LEU* 1.3 75.3 - - - +
87D ILE* 1.3 65.2 + - - +
88D SER* 4.7 7.9 - - - +
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Residues in contact with ILE 87 (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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17D GLU 4.3 0.3 - - - +
18D ALA* 3.1 3.4 - - - +
19D VAL* 2.7 43.6 + - + +
21D LEU* 3.6 26.0 - - + -
71D ARG* 3.7 16.2 - - - +
72D TYR* 3.8 23.1 - - + -
85D LEU* 3.9 8.5 - - + -
86D VAL* 1.3 72.1 - - - +
88D SER* 1.3 62.5 + - - +
90D SER* 4.4 7.6 - - - -
94D ASP* 3.4 24.2 - - + +
98D TYR* 3.7 34.8 - - + +
118D LEU* 3.8 11.4 - - + -
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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