Contacts of the strand formed by residues 84 - 89 (chain B) in PDB entry 3NFP
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 THR 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B GLN* 3.6 5.0 - - - +
37B GLN* 3.0 38.8 + - - +
83B ALA* 1.3 81.0 - - - +
85B TYR* 1.3 65.3 + - - +
86B TYR* 4.1 29.5 - - + +
100B GLY* 4.7 1.6 - - - -
101B THR 3.4 23.3 - - - +
102B LYS* 3.7 18.2 - - + +
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Residues in contact with TYR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLN* 3.1 9.7 - - - +
21B ILE* 5.4 6.7 - - + -
34B TRP* 5.0 10.3 - + + -
35B TYR 3.5 14.6 - - - +
36B GLN* 3.0 32.2 + - + -
46B LEU* 3.8 22.0 - - + -
61B PHE* 4.2 5.1 - + - -
72B LEU* 4.7 16.6 - - + -
74B ILE* 4.2 14.5 - - + +
81B ASP* 2.7 33.1 + - - +
83B ALA* 3.8 19.3 - - + -
84B THR* 1.3 76.9 - - - +
86B TYR* 1.3 62.6 + - - +
100B GLY* 3.4 4.2 - - - -
101B THR* 3.0 41.0 + - - +
103B VAL* 4.0 17.5 - - + -
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Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 3.4 19.5 + - - -
43A GLN 5.1 1.2 + - - -
44A GLY* 4.6 9.1 - - - -
45A LEU* 4.1 29.6 - - + -
6B GLN* 3.5 2.5 - - - +
34B TRP* 3.3 12.2 - - - -
35B TYR* 3.0 45.6 + - + +
37B GLN* 3.4 28.8 + - + -
43B PRO* 5.9 1.1 - - + -
84B THR* 4.1 26.9 - - + +
85B TYR* 1.3 77.9 - - - +
87B CYS* 1.3 65.7 + - - +
97B PHE* 5.2 3.4 - - + -
98B GLY 3.5 20.2 - - - -
99B GLN 3.3 23.2 + - - -
100B GLY* 4.0 6.1 - - - -
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Residues in contact with CYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B MET* 4.5 1.3 - - - -
6B GLN* 3.3 24.8 - - - +
23B CYS* 2.0 49.8 - - + -
32B MET* 3.7 9.6 - - - -
33B HIS 3.3 5.6 - - - +
34B TRP* 3.6 18.1 - - + -
86B TYR* 1.3 73.6 - - - +
88B HIS* 1.3 62.0 + - - +
97B PHE* 3.5 5.9 - - - +
98B GLY* 2.8 33.2 + - - -
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Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 4.8 2.8 - - + +
103A PHE* 3.9 29.8 - + - -
4B MET* 4.7 2.0 - - - -
32B MET* 3.4 9.9 - - - +
33B HIS* 2.9 48.8 + - + +
35B TYR* 4.0 22.5 + - + -
87B CYS* 1.3 79.0 - - - +
89B GLN* 1.3 74.5 + - - +
90B ARG* 4.4 18.6 - - + -
95B LEU* 4.4 10.2 - - + +
96B THR 3.2 27.1 - - - -
97B PHE* 3.5 31.9 - + + -
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ILE* 4.2 18.4 + - + +
4B MET* 3.8 19.0 - - + -
29B ILE* 3.3 33.3 - - + +
31B TYR 4.8 6.5 - - - +
32B MET* 5.0 3.1 - - + -
33B HIS* 5.2 0.2 - - - -
88B HIS* 1.3 92.5 + - - +
90B ARG* 1.3 65.2 + - - +
91B SER* 3.3 15.9 + - - -
92B THR 3.8 11.0 + - - -
94B PRO 3.2 22.0 + - - -
95B LEU* 3.8 4.4 - - - +
96B THR* 2.9 39.3 + - - +
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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