Contacts of the strand formed by residues 88 - 94 (chain A) in PDB entry 2FE4
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LYS 2.9 6.8 + - - +
16A LEU* 3.3 16.2 - - + -
17A VAL 2.9 26.3 + - - -
86A SER* 3.2 7.5 + - - -
87A THR* 1.3 88.4 - - - +
89A ALA* 1.3 68.9 + - - +
90A VAL* 4.0 4.2 + - + -
119A VAL* 5.0 0.4 - - - -
120A ILE* 3.5 19.3 - - + +
122A MET* 5.3 1.1 - - + -
170A VAL* 3.9 30.7 - - + +
174A LEU* 3.4 38.4 - - + -
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Residues in contact with ALA 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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17A VAL* 3.5 6.7 - - + +
19A LEU* 4.6 6.7 - - + -
83A ILE* 5.8 1.6 - - + -
86A SER* 4.6 3.8 - - - +
88A VAL* 1.3 73.8 - - - +
90A VAL* 1.3 63.6 + - - +
91A VAL* 3.7 3.8 + - + -
111A VAL* 3.8 39.5 - - + -
119A VAL* 4.5 2.0 - - + +
120A ILE 3.0 11.3 + - - +
121A ILE* 3.5 7.6 - - + +
122A MET* 3.0 25.1 + - - +
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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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16A LEU* 4.8 9.9 - - + -
17A VAL 2.7 14.5 + - - +
18A PHE* 3.4 45.3 - - + -
19A LEU* 2.7 34.1 + - - +
88A VAL* 4.3 15.3 - - + -
89A ALA* 1.3 75.6 - - - +
91A VAL* 1.3 54.7 + - - +
92A VAL* 3.7 5.7 + - + +
122A MET* 3.5 8.7 - - + +
124A VAL* 3.6 28.9 - - + -
166A LEU* 4.4 9.0 - - + -
167A PHE* 6.0 0.4 - - + -
170A VAL* 4.9 5.6 - - + -
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Residues in contact with VAL 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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19A LEU* 3.4 17.9 - - + +
89A ALA 4.6 3.4 - - - +
90A VAL* 1.3 71.5 - - - +
92A VAL* 1.3 57.4 + - - +
104A THR* 3.8 34.3 - - + +
107A TRP* 4.1 27.4 - - + -
108A ILE* 4.1 19.1 - - + +
111A VAL* 4.8 4.3 - - + -
121A ILE* 4.3 13.7 - - + -
122A MET 2.9 11.9 + - - +
123A LEU* 3.5 13.2 - - + +
124A VAL 2.8 29.7 + - - -
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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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18A PHE* 4.2 8.5 - - + -
19A LEU 2.7 17.6 + - - +
20A GLY* 3.5 19.2 - - - -
21A GLU 4.1 0.9 + - - -
24A VAL* 3.6 26.8 - - + +
26A LYS* 4.1 11.9 - - + -
29A LEU* 4.0 13.9 - - + -
90A VAL* 4.0 22.7 - - + +
91A VAL* 1.3 77.4 - - - +
93A TYR* 1.3 75.8 + - - +
100A SER 4.7 0.9 - - - +
104A THR* 4.6 5.6 - - - +
124A VAL* 3.5 12.8 - - + +
126A ASN* 3.9 16.8 - - + -
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Residues in contact with TYR 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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24A VAL* 3.5 12.7 - - - +
92A VAL* 1.3 78.8 - - - +
94A ASP* 1.3 68.8 + - - +
95A ILE* 4.0 9.8 - - + +
100A SER* 3.3 25.8 - - - +
101A PHE* 3.6 37.4 - + + -
104A THR* 3.8 3.1 - - + -
123A LEU* 4.0 28.9 - - + -
124A VAL 2.9 21.2 + - - -
125A GLY* 3.5 23.3 - - - -
126A ASN* 3.0 25.3 + - - +
136A ILE* 3.8 19.2 - - + +
137A THR 4.9 0.3 + - - -
141A GLY* 3.7 9.9 - - - -
152A PHE* 3.3 23.9 - + - -
154A GLU* 4.5 4.5 + - - -
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Residues in contact with ASP 94 (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 SER 4.4 1.3 - - - +
24A VAL* 3.6 19.0 - - + +
93A TYR* 1.3 75.5 - - - +
95A ILE* 1.3 56.1 + - - +
96A THR* 2.6 33.7 + - - +
97A ASN* 2.7 40.9 + - + +
100A SER* 2.8 18.9 + - - +
126A ASN 3.8 4.5 - - - -
127A LYS* 3.1 39.1 + - + +
136A ILE* 3.6 2.4 - - - +
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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