Contacts of the strand formed by residues 164 - 171 (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 TRP 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.9 0.9 - - - -
60A PHE* 2.8 40.0 + - - +
81A VAL* 3.4 28.3 - - + -
82A CYS* 3.4 22.2 - - - -
83A LYS* 3.6 23.1 - - + -
96A SER 6.1 0.7 - - - -
99A GLY* 3.5 24.9 - - - -
101A LEU* 3.4 28.3 - - + -
134A LEU* 3.9 29.2 - - + -
136A VAL* 5.0 4.5 - - + -
158A ILE* 3.8 16.7 - - + +
159A PRO* 3.0 43.0 + - + -
160A VAL* 4.3 9.0 - - + +
162A GLU 4.1 10.4 + - - -
163A PRO* 1.3 73.5 - - - +
165A ARG* 1.3 61.8 + - - +
166A PRO* 3.8 0.9 - - - +
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Residues in contact with ARG 165 (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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15A ASP* 3.6 20.6 + - - +
18A THR* 4.8 0.2 - - - +
55A LEU* 4.0 32.2 - - + +
56A GLY 2.6 25.1 + - - -
57A THR* 3.2 17.3 + - - +
58A PRO 2.5 25.0 + - - -
59A ARG* 3.4 44.5 - - - +
81A VAL* 3.3 2.8 - - - -
82A CYS* 2.9 38.0 + - - +
84A GLU* 3.5 34.8 + - + -
88A ARG* 4.4 5.9 - - - +
163A PRO* 5.0 0.7 - - - -
164A TRP* 1.3 73.0 - - - +
166A PRO* 1.3 70.9 - - + +
167A PHE 3.2 0.2 + - - -
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Residues in contact with PRO 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A MSE 3.7 29.6 - - + -
55A LEU* 3.2 8.5 - - - +
56A GLY* 2.8 42.3 + - - +
58A PRO* 3.7 21.5 - - + +
60A PHE* 3.8 15.0 - - + -
67A TRP* 4.1 11.2 - - + -
80A GLY 3.5 7.6 - - - +
81A VAL* 4.2 4.2 - - + -
164A TRP 3.8 5.6 - - - +
165A ARG* 1.3 83.9 - - + +
167A PHE* 1.3 58.7 + - - +
168A PHE* 3.9 11.0 - - + -
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Residues in contact with PHE 167 (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* 4.0 10.8 - + - -
53A CYS* 3.8 38.4 - - + -
54A VAL 4.0 0.9 - - - -
55A LEU* 3.6 17.3 - - + -
78A ASP* 4.2 16.6 - - + -
79A VAL* 3.8 1.6 - - - +
80A GLY 2.6 38.8 + - - +
81A VAL* 3.9 11.7 - - - +
82A CYS* 3.8 10.8 - - + +
92A ILE* 4.9 3.1 - - + -
94A LEU* 3.8 23.8 - - + -
100A PHE* 3.7 21.5 - + - -
102A THR* 3.6 18.2 - - + -
165A ARG 3.2 0.8 + - - +
166A PRO* 1.3 70.8 - - - +
168A PHE* 1.3 91.9 + - - +
169A ALA* 4.3 2.7 - - + -
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Residues in contact with PHE 168 (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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12A MSE 4.4 3.4 - - - -
14A PHE* 3.4 32.8 - + + -
32A PHE* 3.5 21.1 - + + -
53A CYS* 3.3 6.9 - - - +
54A VAL 3.1 38.2 + - - +
56A GLY* 3.7 23.8 - - - -
67A TRP* 4.2 16.6 - + - -
69A VAL* 3.5 41.3 - - + -
78A ASP 3.5 6.3 - - - -
79A VAL* 4.7 3.8 - - + -
166A PRO* 3.9 11.4 - - + -
167A PHE* 1.3 95.5 - - - +
169A ALA* 1.3 63.7 + - - +
181A LEU* 4.6 3.4 - - + -
183A ILE* 4.1 16.2 - - + -
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Residues in contact with ALA 169 (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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32A PHE* 4.2 3.1 - - - -
52A LEU 3.4 14.4 - - - +
53A CYS* 4.3 6.5 - - - +
77A TRP* 3.4 22.0 - - - +
78A ASP* 3.0 34.8 + - + +
167A PHE* 4.3 8.5 - - + -
168A PHE* 1.3 77.9 - - - +
170A HIS* 1.3 65.5 + - - +
181A LEU* 3.4 6.9 - - - +
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Residues in contact with HIS 170 (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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23A LEU* 4.2 1.4 - - - +
32A PHE* 4.2 15.7 - - + -
33A ARG* 4.0 9.9 - - + -
34A SER* 3.3 29.5 + - - +
52A LEU* 3.2 29.0 + - - +
74A SER* 3.4 24.0 + - - -
76A VAL* 3.5 9.0 - - - +
77A TRP* 4.5 0.2 - - - +
169A ALA* 1.3 78.3 - - - +
171A LYS* 1.3 63.0 + - - +
172A ARG* 3.4 31.9 - - + -
179A SER* 3.2 28.5 + - - -
180A ILE* 4.7 3.8 - - - -
181A LEU* 3.7 22.4 - - + -
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Residues in contact with LYS 171 (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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34A SER* 3.5 4.9 - - - +
52A LEU* 3.7 21.8 - - + +
74A SER* 4.7 0.7 + - - -
75A GLN* 5.2 1.6 + - - +
76A VAL* 3.4 44.0 + - + +
170A HIS* 1.3 84.7 + - - +
172A ARG* 1.3 77.7 + - - +
173A GLY 3.8 0.2 + - - -
177A ASP* 4.7 0.3 - - - +
179A SER* 5.4 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