Contacts of the strand formed by residues 23 - 27 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16Z GLU* 4.1 12.6 - - - +
17Z LEU* 3.2 20.3 - - + +
19Z ARG* 6.3 0.2 - - - +
20Z ASP* 3.5 26.2 - - + +
21Z GLU 3.1 0.6 - - - -
22Z LYS* 1.3 78.4 - - - +
24Z PHE* 1.3 62.2 + - - +
51Z ARG* 2.9 34.3 + - - -
75Z ARG* 3.6 24.5 - - + +
77Z ILE* 3.7 28.9 - - + -
161Z ILE* 4.1 19.5 - - + -
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Residues in contact with PHE 24 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150Y LEU* 3.8 29.2 - - + -
154Y TYR* 3.9 15.7 - + + +
17Z LEU* 4.1 6.3 - - - -
22Z LYS 3.8 11.7 - - - -
23Z VAL* 1.3 75.7 - - - +
25Z LEU* 1.3 71.5 + - - +
26Z LEU* 4.2 17.0 - - + -
50Z LYS 5.0 0.2 - - - -
51Z ARG* 3.4 21.3 - - - +
53Z ILE* 3.9 15.3 - - + -
66Z ALA* 5.2 2.5 - - - -
69Z ALA* 3.9 8.5 - - + -
74Z LEU* 3.7 28.7 - - + -
75Z ARG 3.7 1.4 + - - -
76Z PRO* 3.4 29.6 - - + +
77Z ILE* 2.8 30.3 + - - +
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Residues in contact with LEU 25 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Z MET* 4.3 13.7 - - + -
17Z LEU* 5.3 4.0 - - + -
24Z PHE* 1.3 78.4 - - - +
26Z LEU* 1.3 65.6 + - - +
30Z VAL* 4.2 16.6 - - + -
40Z SER* 3.9 27.4 - - - -
43Z LEU* 4.5 4.3 - - + -
51Z ARG 2.8 8.1 + - - +
52Z ILE* 3.8 28.0 - - + +
53Z ILE* 3.1 24.0 + - - +
77Z ILE* 3.1 44.6 - - + +
79Z GLU* 4.5 8.5 - - + -
115Z ARG* 4.2 16.2 - - - +
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Residues in contact with LEU 26 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150Y LEU* 5.5 1.1 - - + -
185Y TRP* 4.7 9.2 - - + -
24Z PHE* 4.2 21.5 - - + -
25Z LEU* 1.3 77.9 - - - +
27Z GLY* 1.3 58.9 + - - +
30Z VAL* 4.3 6.1 - - - -
53Z ILE* 3.4 21.8 - - + +
55Z THR* 4.1 13.5 - - + -
62Z PHE* 4.2 24.0 - - + +
65Z ILE* 4.5 15.5 - - + -
66Z ALA* 3.8 24.5 - - + -
76Z PRO* 4.6 0.7 - - + -
77Z ILE 2.8 12.6 + - - +
78Z CYS* 3.4 14.1 - - + +
79Z GLU 2.9 24.1 + - - +
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Residues in contact with GLY 27 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Z LEU* 1.3 76.8 - - - +
28Z GLU* 1.3 64.5 + - - -
30Z VAL* 3.7 12.0 - - - +
53Z ILE 3.3 7.0 + - - +
54Z ASP* 3.5 3.1 - - - -
55Z THR* 2.9 32.9 + - - +
62Z PHE* 4.5 6.3 - - - -
79Z GLU 3.5 14.6 - - - -
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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