Contacts of the strand formed by residues 87 - 95 (chain F) in PDB entry 6NQN
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 TYR 87 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65F ASN* 2.7 34.2 + - - -
66F ARG* 3.0 19.2 + - - +
67F VAL 3.9 0.2 + - - -
78F TYR* 5.3 10.1 - + + -
79F PHE* 3.6 34.5 - + + -
82F SER* 4.0 16.8 - - - +
83F PHE* 4.0 24.9 - + - -
86F GLY* 1.3 76.1 - - - +
88F SER* 1.3 72.7 + - - +
89F TRP* 4.0 21.6 - + + -
106F ASP* 4.5 2.3 - - - +
107F ILE* 2.9 48.3 + - + +
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Residues in contact with SER 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F TYR* 1.3 85.1 - - - +
89F TRP* 1.3 67.5 + - - +
90F GLU* 5.1 6.8 + - - +
105F ASN 3.2 13.2 - - - -
106F ASP* 3.7 19.5 - - - -
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Residues in contact with TRP 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F VAL* 3.8 35.2 - - + -
63F KZ4 2.7 33.2 + - - -
66F ARG* 5.8 1.8 - - - -
87F TYR* 4.0 24.5 - + + -
88F SER* 1.3 77.1 - - - +
90F GLU* 1.3 78.5 + - - +
91F ARG* 3.5 51.8 - - + -
103F ALA* 3.6 19.3 - - + -
104F THR* 3.3 4.6 - - - -
105F ASN* 2.9 57.5 + - + +
107F ILE* 4.2 4.9 - - + -
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Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F SER* 5.1 6.9 + - - +
89F TRP* 1.3 85.3 - - - +
91F ARG* 1.3 64.2 + - - +
103F ALA 3.4 7.4 - - - +
104F THR* 4.2 14.8 - - + -
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Residues in contact with ARG 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F THR* 2.8 41.8 + - - -
60F VAL* 4.1 1.0 - - - +
63F KZ4 2.7 31.5 + - - +
66F ARG* 3.5 13.7 - - - +
89F TRP* 3.5 37.6 - - + -
90F GLU* 1.3 78.4 - - - +
92F SER* 1.3 71.1 + - - +
93F MET* 3.7 28.9 - - + -
101F CYS 3.9 0.3 - - - +
102F ASN* 3.3 5.9 - - - +
103F ALA 2.8 34.4 + - - +
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Residues in contact with SER 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ARG* 1.3 78.0 - - - +
93F MET* 1.3 61.7 + - - +
94F ASN* 4.0 3.4 + - - +
100F ILE* 3.4 21.8 - - - +
101F CYS 3.5 4.0 - - - -
102F ASN* 3.1 18.9 + - - -
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Residues in contact with MET 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F ILE 4.7 7.9 - - - +
59F THR* 3.9 17.5 - - - -
60F VAL* 3.9 13.5 - - + -
91F ARG* 3.7 32.8 - - + -
92F SER* 1.3 72.7 + - - +
94F ASN* 1.3 59.6 + - - +
95F TYR* 3.6 25.6 - - + +
100F ILE* 3.4 7.3 - - - -
101F CYS* 2.8 55.4 + - + +
103F ALA* 3.8 28.7 - - + +
120F PHE* 4.3 1.1 - - + -
139F TRP* 6.0 4.5 - - + -
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Residues in contact with ASN 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F SER* 4.0 3.8 + - - +
93F MET* 1.3 69.8 - - - +
95F TYR* 1.3 73.9 + - - +
96F GLU 4.0 0.2 + - - -
98F GLY* 4.9 5.2 - - - +
99F GLY 4.0 4.8 - - - +
100F ILE* 4.3 21.8 - - + +
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Residues in contact with TYR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F ILE* 3.5 31.2 + - + +
93F MET* 3.6 26.6 - - + +
94F ASN* 1.3 85.1 - - - +
96F GLU* 1.3 65.1 + - - +
97F ASP* 3.2 15.0 - - - +
98F GLY* 3.1 13.2 + - - -
99F GLY 2.9 22.3 + - - +
101F CYS* 4.1 8.6 - - - -
125F PHE* 3.6 28.0 - + + -
131F VAL* 5.1 5.6 - - + -
139F TRP* 3.4 40.0 - + - -
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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