Contacts of the strand formed by residues 23 - 27 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154U TYR* 3.5 0.2 + - - -
16V GLU* 4.2 9.2 - - + +
17V LEU* 3.2 19.9 - - + +
19V ARG* 6.0 0.4 - - - +
20V ASP* 2.9 29.4 + - + +
22V LYS* 1.3 77.1 - - - +
24V PHE* 1.3 64.8 + - - +
51V ARG* 3.0 29.8 + - - -
75V ARG* 3.6 37.5 - - + +
77V ILE* 3.9 20.0 - - + -
161V ILE* 4.0 19.1 - - + -
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Residues in contact with PHE 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150U LEU* 4.1 12.1 - - + -
154U TYR* 4.0 18.2 - + + +
17V LEU* 4.0 7.0 - - - -
22V LYS 4.0 8.7 - - - -
23V VAL* 1.3 79.9 - - - +
25V LEU* 1.3 59.8 + - - +
26V LEU* 4.0 21.1 - - + -
51V ARG* 3.3 21.5 - - - +
53V ILE* 3.7 28.5 - - + -
66V ALA* 5.5 0.4 - - - -
69V ALA* 3.7 17.0 - - + -
74V LEU* 3.7 28.3 - - + -
75V ARG 3.7 1.2 + - - -
76V PRO* 3.5 28.6 - - + +
77V ILE* 2.8 38.5 + - - +
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Residues in contact with LEU 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V MET* 4.1 15.5 - - + -
17V LEU* 5.1 4.0 - - + -
24V PHE* 1.3 75.5 - - - +
26V LEU* 1.3 61.7 + - - +
30V VAL* 3.6 31.0 - - + -
40V SER* 3.9 21.3 - - - -
43V LEU* 4.7 5.8 - - + -
51V ARG 2.8 11.2 + - - +
52V ILE* 3.5 25.4 - - + +
53V ILE* 2.9 26.2 + - - +
77V ILE* 3.4 38.1 - - + +
79V GLU* 4.6 7.6 - - + +
115V ARG* 4.2 8.7 - - - +
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Residues in contact with LEU 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150U LEU* 5.2 1.1 - - + -
185U TRP* 4.8 10.1 - - + -
24V PHE* 4.0 23.6 - - + -
25V LEU* 1.3 76.3 - - - +
27V GLY* 1.3 59.2 + - - +
30V VAL* 4.3 5.2 - - - -
53V ILE* 3.4 22.0 - - + +
55V THR* 4.0 12.3 - - + -
62V PHE* 4.4 13.9 - - + +
65V ILE* 4.3 23.1 - - + -
66V ALA* 3.8 18.4 - - + -
76V PRO* 4.5 1.8 - - + -
77V ILE 3.0 11.7 + - - +
78V CYS* 3.5 21.7 - - + -
79V GLU* 2.8 25.3 + - - +
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Residues in contact with GLY 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26V LEU* 1.3 77.3 - - - +
28V GLU* 1.3 62.7 + - - -
30V VAL* 3.5 15.3 - - - +
53V ILE 3.3 7.2 + - - +
55V THR* 2.8 33.6 + - - +
62V PHE* 4.3 6.1 - - - -
79V GLU 3.7 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