Contacts of the strand formed by residues 76 - 83 (chain A) in PDB entry 2FBE
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 VAL 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A SER* 3.3 8.0 + - - -
75A GLN* 1.3 89.6 - - + +
77A TRP* 1.3 67.4 + - - +
105A CYS 3.4 7.6 - - - +
106A ARG* 4.0 23.3 - - - +
107A GLU* 4.2 18.2 - - + +
170A HIS* 3.5 2.1 - - - -
171A LYS* 3.4 55.8 + - + +
172A ARG 5.2 3.6 - - - +
173A GLY* 6.1 1.1 - - - -
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Residues in contact with TRP 77 (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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71A VAL* 3.7 36.5 - - + +
74A SER* 3.3 40.7 + - - +
76A VAL* 1.3 79.5 - - - +
78A ASP* 1.3 78.5 + - - +
79A VAL* 3.9 13.7 - - + -
103A VAL* 4.0 24.2 - - + -
105A CYS* 2.8 42.3 + - + +
106A ARG* 3.1 3.0 + - - -
111A PHE* 3.4 35.9 - + - -
127A LEU* 4.1 6.5 - - + -
130A VAL* 3.9 26.9 - - + -
169A ALA 3.4 16.6 - - - +
181A LEU* 4.4 11.0 - - + -
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Residues in contact with ASP 78 (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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77A TRP* 1.3 90.6 - - - +
79A VAL* 1.3 68.3 + - - +
94A LEU* 2.9 24.2 - - + +
102A THR* 4.5 5.9 + - - +
103A VAL 3.4 5.5 - - - +
104A GLY* 2.9 16.6 + - - -
106A ARG* 2.8 29.7 + - - -
167A PHE* 4.2 12.6 - - + -
168A PHE* 3.5 3.3 - - - -
169A ALA* 3.0 45.0 + - + +
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Residues in contact with VAL 79 (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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69A VAL* 3.9 33.7 - - + -
71A VAL* 4.6 4.5 - - + -
77A TRP* 3.9 21.5 - - + -
78A ASP* 1.3 82.0 - - - +
80A GLY* 1.3 63.5 + - - +
102A THR* 3.0 8.9 - - - -
103A VAL* 2.8 35.8 + - + +
130A VAL* 4.8 7.2 - - + -
132A ILE* 3.0 28.9 - - + -
143A PHE* 3.6 5.7 - - + -
167A PHE 3.8 9.6 - - - +
168A PHE* 4.7 3.4 - - + -
181A LEU* 4.7 7.6 - - + -
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Residues in contact with GLY 80 (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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67A TRP* 4.0 6.8 + - - -
79A VAL* 1.3 84.8 - - - +
81A VAL* 1.3 65.3 + - - +
101A LEU 3.4 8.5 - - - -
102A THR* 4.3 0.7 - - - -
132A ILE* 4.2 3.6 - - - -
141A ILE* 4.7 1.1 - - - -
143A PHE* 3.8 15.0 - - - -
166A PRO* 3.5 2.9 - - - +
167A PHE* 2.6 33.5 + - - +
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Residues in contact with VAL 81 (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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60A PHE* 5.5 0.2 - - + -
67A TRP* 3.7 27.4 - - + -
80A GLY* 1.3 79.9 - - - +
82A CYS* 1.3 62.3 + - - +
99A GLY 4.0 0.2 - - - +
100A PHE* 3.8 0.5 - - - -
101A LEU* 2.9 41.1 + - + +
102A THR* 4.0 2.4 - - - +
134A LEU* 4.6 5.6 - - + -
141A ILE* 3.5 23.6 - - + -
164A TRP* 3.4 37.9 - - + -
165A ARG 3.3 14.6 - - - +
166A PRO* 4.2 2.7 - - + -
167A PHE* 3.8 3.8 - - - +
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Residues in contact with CYS 82 (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 PHE* 5.5 0.9 - - - -
55A LEU* 3.6 33.4 - - - -
81A VAL* 1.3 73.6 - - - +
83A LYS* 1.3 70.3 + - - +
86A VAL* 4.2 9.2 - - + -
99A GLY 3.1 8.3 - - - +
100A PHE* 3.5 31.2 - - + -
164A TRP* 3.4 7.9 - - - -
165A ARG* 2.9 38.7 + - - -
167A PHE* 3.8 8.7 - - + -
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Residues in contact with LYS 83 (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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55A LEU* 5.9 0.2 - - - +
82A CYS* 1.3 75.9 - - - +
84A GLU* 1.3 63.9 + - - +
85A SER* 3.0 5.7 + - - +
86A VAL* 3.0 35.9 + - + +
88A ARG* 5.3 0.2 + - - -
98A HIS 5.7 0.2 - - - -
99A GLY* 3.0 25.7 + - - +
159A PRO* 3.6 35.5 - - - +
161A CYS* 6.6 0.2 - - - -
162A GLU* 3.3 34.2 + - + +
163A PRO 4.0 4.9 - - - -
164A TRP* 3.8 21.5 - - + -
165A ARG* 4.9 0.2 - - - -
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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