Contacts of the strand formed by residues 85 - 92 (chain E) in PDB entry 2F53
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 SER 85 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E ARG* 3.7 15.6 - - - +
35E GLN 3.0 20.5 + - - -
36E ASP* 2.7 23.4 + - - +
37E PRO* 5.1 4.9 - - - -
83E GLN 3.1 8.6 + - - -
84E THR* 1.3 79.1 - - - +
86E VAL* 1.3 70.0 + - - +
87E TYR* 3.7 13.4 - - - -
106E SER 3.7 1.2 - - - +
107E ARG* 3.7 2.1 - - - +
108E LEU 3.1 30.1 + - - +
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Residues in contact with VAL 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ARG* 3.3 1.6 - - - -
35E GLN* 2.7 47.6 + - + +
37E PRO* 5.2 13.2 - - + -
85E SER* 1.3 80.6 + - - +
87E TYR* 1.3 62.6 + - - +
88E PHE* 3.6 27.6 + - + -
106E SER 3.3 11.2 - - - +
107E ARG* 3.7 39.5 - - + +
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Residues in contact with TYR 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLN* 3.2 7.1 + - - -
19E LEU* 3.9 24.0 - - + -
32E TRP* 4.0 6.7 - - + -
33E TYR 3.2 15.0 - - - +
34E ARG* 3.7 6.2 + - + -
44E ILE* 3.7 14.4 - - + -
62E TYR* 2.8 43.6 + + - -
74E LEU* 4.0 11.2 - - + -
76E LEU* 5.1 0.4 - - + -
83E GLN* 2.4 37.1 + - - +
85E SER* 3.7 26.2 - - - -
86E VAL* 1.3 75.8 - - - +
88E PHE* 1.3 61.8 + - - +
105E GLY* 3.2 2.3 - - - -
106E SER* 2.7 45.7 + - - +
108E LEU* 4.0 20.4 - - + +
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Residues in contact with PHE 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLN* 4.1 5.6 - - - -
41D LYS 4.1 2.9 - - - -
42D GLY* 3.7 30.7 - - - -
43D LEU* 4.0 14.4 - - + -
4E GLN* 3.4 1.6 - - - -
31E SER 3.9 0.2 - - - +
32E TRP* 3.6 5.0 - - - -
33E TYR* 2.8 43.2 + - + +
35E GLN* 3.3 25.8 - - + -
41E LEU* 4.0 16.2 - - + -
86E VAL* 3.6 27.6 - - + -
87E TYR* 1.3 76.2 - - - +
89E CYS* 1.3 61.0 + - - +
102E PHE* 3.9 22.2 - + + -
103E GLY 3.6 13.2 - - - -
104E GLU 3.9 1.3 - - - -
105E GLY* 3.5 25.4 - - - -
107E ARG* 4.6 1.6 - - - -
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Residues in contact with CYS 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E VAL* 4.0 3.0 - - + +
4E GLN* 2.9 12.3 + - + +
21E CYS* 2.0 54.1 - - + -
30E MET* 4.2 9.9 - - - -
31E SER 3.1 14.6 - - - +
32E TRP* 3.7 20.2 - - + -
72E PHE* 5.0 0.9 - - - -
88E PHE* 1.3 77.0 - - - +
90E ALA* 1.3 65.4 + - - +
91E SER* 5.6 0.2 - - - -
101E PHE 3.8 0.3 - - - +
102E PHE* 3.4 3.7 - - - -
103E GLY 2.7 28.9 + - - -
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Residues in contact with ALA 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E VAL* 5.3 0.2 - - - -
29E TYR* 4.4 1.0 - - - -
30E MET* 3.4 1.8 - - - -
31E SER* 2.8 51.6 + - - +
33E TYR* 4.2 5.4 - - + -
88E PHE 4.1 0.2 + - - -
89E CYS* 1.3 77.3 - - - +
91E SER* 1.3 61.9 + - - +
100E LEU* 4.0 18.6 - - + -
101E PHE 3.1 10.3 - - - +
102E PHE* 3.8 25.6 - - + -
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Residues in contact with SER 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E VAL* 3.4 20.6 - - - +
23E GLN* 3.8 8.2 - - - +
27E HIS* 2.7 25.5 + - - -
29E TYR* 3.1 15.9 - - - -
30E MET* 3.9 16.8 - - - -
89E CYS* 5.6 0.4 - - - -
90E ALA* 1.3 76.9 - - - +
92E SER* 1.3 63.6 + - - +
100E LEU* 4.2 2.7 - - - -
101E PHE* 2.8 33.7 + - - +
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Residues in contact with SER 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ARG* 3.3 32.8 + - - -
27E HIS* 3.2 19.2 + - - +
29E TYR* 3.0 34.9 + - - +
91E SER* 1.3 75.6 - - - +
93E TYR* 1.3 72.2 + - - +
98E GLY 4.0 1.1 - - - -
99E GLU 3.2 24.2 - - - -
100E LEU* 4.0 2.7 - - - -
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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