Contacts of the strand formed by residues 23 - 27 (chain F) in PDB entry 3EXG
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 23 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154E TYR* 3.6 0.2 + - - -
16F GLU* 4.1 14.1 - - + +
17F LEU* 3.2 20.3 - - + +
19F ARG* 6.1 0.4 - - - +
20F ASP* 3.0 24.1 + - + +
22F LYS* 1.3 76.2 - - - +
24F PHE* 1.3 64.5 + - - +
51F ARG* 3.1 27.7 + - - -
75F ARG* 3.5 40.4 - - + +
77F ILE* 4.4 17.3 - - + -
161F ILE* 4.3 18.6 - - + -
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Residues in contact with PHE 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E LEU* 4.1 13.9 - - + -
154E TYR* 4.0 18.2 - + + +
17F LEU* 4.1 6.7 - - - -
22F LYS 4.0 8.3 - - - -
23F VAL* 1.3 80.3 - - - +
25F LEU* 1.3 66.0 + - - +
26F LEU* 4.2 15.7 - - + -
51F ARG* 3.4 22.4 - - - +
53F ILE* 3.8 29.2 - - + -
66F ALA* 5.5 1.1 - - - -
69F ALA* 3.9 17.3 - - + -
74F LEU* 3.7 29.2 - - + -
75F ARG 3.7 1.8 + - - -
76F PRO* 3.4 28.7 - - + +
77F ILE* 2.8 31.3 + - - +
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Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F MET* 4.5 11.0 - - + -
17F LEU* 5.2 4.5 - - + -
24F PHE* 1.3 77.8 - - - +
26F LEU* 1.3 64.4 + - - +
30F VAL* 3.6 27.1 - - + -
40F SER* 4.0 19.3 - - - -
43F LEU* 5.0 1.8 - - + -
51F ARG 2.8 9.4 + - - +
52F ILE* 3.8 30.0 - - + +
53F ILE* 2.8 28.2 + - - +
77F ILE* 3.5 35.0 - - + +
79F GLU* 4.3 11.0 - - + -
115F ARG* 4.2 15.9 - - - +
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Residues in contact with LEU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E LEU* 5.2 0.9 - - + -
185E TRP* 4.6 11.7 - - + -
24F PHE* 4.2 22.0 - - + -
25F LEU* 1.3 77.8 - - - +
27F GLY* 1.3 58.7 + - - +
30F VAL* 4.3 4.3 - - - -
53F ILE* 3.4 22.7 - - + +
55F THR* 4.2 12.6 - - + -
62F PHE* 4.4 13.7 - - + +
65F ILE* 4.3 22.9 - - + -
66F ALA* 3.8 24.9 - - + -
76F PRO* 4.6 1.1 - - + -
77F ILE 3.1 18.0 + - - +
78F CYS* 3.5 7.6 - - + +
79F GLU 3.0 23.9 + - - +
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Residues in contact with GLY 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F LEU* 1.3 76.1 - - - +
28F GLU* 1.3 63.4 + - - -
30F VAL* 3.6 12.6 - - - +
53F ILE 3.1 6.7 + - - +
54F ASP* 3.4 2.4 - - - -
55F THR* 2.9 33.8 + - - +
62F PHE* 4.3 6.5 - - - -
79F GLU 3.6 15.3 - - - -
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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