Contacts of the strand formed by residues 86 - 94 (chain A) in PDB entry 2FBI
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 ASP 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ALA* 2.9 24.4 + - + +
84A PRO 3.5 1.0 + - - -
85A LYS* 1.3 80.0 - - - +
87A GLN* 1.3 58.2 + - - +
88A ARG* 3.1 30.1 + - - +
89A ARG* 3.1 44.4 + - + +
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LYS* 3.1 65.4 + - - +
83A ALA 3.6 10.6 + - - +
84A PRO* 3.5 27.7 + - - +
86A ASP* 1.3 71.1 + - - +
88A ARG* 1.3 62.4 + - + +
89A ARG 3.3 2.9 - - - -
90A VAL* 5.1 0.7 - - - +
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP* 3.1 14.0 + - - +
87A GLN* 1.3 79.9 - - + +
89A ARG* 1.3 76.4 + - - +
90A VAL* 4.2 5.1 + - - +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU* 3.9 27.4 + - + +
82A LYS* 3.4 7.4 - - - -
83A ALA* 3.3 23.7 + - + -
86A ASP* 3.1 41.2 + - + +
87A GLN 3.8 1.9 - - - +
88A ARG* 1.3 99.7 + - - +
90A VAL* 1.3 62.8 + - - +
91A TYR* 4.1 17.7 - - + +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU* 3.5 4.1 + - - +
51A SER* 2.8 48.0 + - - +
80A ARG* 4.2 27.6 - - + -
81A TRP 3.6 8.5 - - - +
82A LYS* 4.3 15.3 - - + -
87A GLN 5.1 0.4 - - - +
88A ARG 4.2 6.0 + - - +
89A ARG* 1.3 82.1 - - - +
91A TYR* 1.3 67.8 + - - +
92A VAL* 4.9 0.2 - - + -
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLU* 4.4 9.6 - - + -
49A MET* 3.4 13.9 - - - +
50A GLU* 3.6 37.1 - - + +
80A ARG* 3.3 6.1 - - - -
81A TRP* 2.9 73.5 + + + +
83A ALA* 4.0 29.6 - - + -
89A ARG* 4.1 13.3 - - + +
90A VAL* 1.3 76.8 - - - +
92A VAL* 1.3 62.1 - - - +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.4 23.8 - - + +
48A GLU* 3.1 5.8 - - - -
49A MET 2.8 35.9 + - - +
51A SER* 4.0 26.5 - - - -
54A LEU* 3.9 19.3 - - + -
69A LEU* 4.1 15.5 - - + -
78A VAL* 4.0 15.7 - - + -
79A ARG 3.5 9.6 - - - +
80A ARG* 4.0 14.8 - - + -
90A VAL* 4.9 0.7 - - + -
91A TYR* 1.3 80.2 - - - +
93A ASN* 1.3 65.4 + - - +
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Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 4.3 10.8 - - - -
47A GLY 5.1 0.7 - - - -
48A GLU* 3.8 22.9 - - + +
78A VAL* 3.1 5.5 - - - -
79A ARG* 2.9 48.5 + - - +
81A TRP* 2.6 35.6 + - - -
92A VAL* 1.3 77.3 - - - +
94A LEU* 1.3 86.1 + - - +
95A THR* 4.8 0.6 - - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ILE* 3.8 31.2 - - + +
43A LEU* 3.8 14.6 + - + +
44A ARG* 3.5 36.3 - - + +
77A ILE* 3.4 29.4 - - + +
78A VAL* 4.2 8.1 - - + -
93A ASN* 1.3 91.2 + - - +
95A THR* 1.3 66.4 + - - +
98A GLY* 4.3 4.9 - - - +
99A GLN* 3.7 38.2 + - + +
102A PHE* 5.2 0.4 - - + -
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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