Contacts of the strand formed by residues 25 - 31 (chain B) in PDB entry 3PGE
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 LEU 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B VAL* 4.3 11.2 - - - +
24B GLN* 1.3 112.7 - - + +
26B VAL* 1.3 61.4 + - - +
39B ALA* 4.6 2.8 - - - +
70B MET 3.5 5.8 - - - +
71B ASP* 4.1 10.3 - - - +
119B MET* 3.7 21.3 - - + -
120B ASP 5.7 1.1 - - - +
121B ILE* 3.4 35.8 - - + +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 4.1 11.0 - - + -
23B VAL* 5.4 2.5 - - + -
24B GLN 4.8 0.4 - - - -
25B LEU* 1.3 75.8 - - - +
27B ASN* 1.3 74.5 + - - +
28B PHE* 3.8 15.6 + - + -
37B ALA* 3.7 21.1 - - + -
38B GLN 4.6 5.6 - - - +
39B ALA* 4.3 16.6 - - + -
68B LEU 3.8 0.3 - - - +
69B GLY* 3.7 0.2 - - - -
70B MET 3.0 27.7 + - - +
72B LEU* 3.4 44.0 - - + -
121B ILE* 3.9 4.9 - - - -
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Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 1.3 80.0 - - - +
28B PHE* 1.3 59.8 + - - +
29B GLN* 3.7 12.6 + - + +
37B ALA* 3.8 11.6 - - - +
38B GLN 4.5 7.9 + - - +
67B THR* 3.9 22.7 - - + +
68B LEU 3.6 2.7 - - - -
69B GLY* 3.2 22.3 + - - -
119B MET 5.0 0.2 - - - +
121B ILE* 3.0 47.1 + - - +
122B ASP 4.4 6.5 + - - -
123B ALA* 4.6 8.7 - - - +
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Residues in contact with PHE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 5.0 9.4 - + - -
16B ILE* 3.9 24.9 - - + -
19B PHE* 4.1 7.9 - + - -
26B VAL* 3.9 20.0 - - + -
27B ASN* 1.3 70.7 - - - +
29B GLN* 1.3 61.8 + - - +
30B CYS* 5.0 0.2 - - - -
35B ILE* 4.2 21.1 - - + -
36B ILE 3.7 1.8 - - - -
37B ALA* 3.8 20.9 - - + -
50B LEU* 4.0 15.5 - - + -
52B ILE* 6.3 0.2 - - + -
67B THR* 3.5 2.5 - - - -
68B LEU* 2.9 54.9 + - + +
70B MET* 3.5 42.4 - - + -
72B LEU* 4.0 14.6 - - + -
75B LEU* 4.7 1.1 - - + -
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Residues in contact with GLN 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASN* 4.4 13.1 - - + +
28B PHE* 1.3 74.5 - - - +
30B CYS* 1.3 62.7 + - - +
31B LYS* 3.4 30.3 - - - +
34B GLY 3.9 0.9 - - - +
35B ILE* 3.4 2.7 - - - -
36B ILE* 2.8 62.0 + - + +
38B GLN* 4.9 8.3 + - - +
66B VAL 3.7 3.1 - - - -
67B THR* 3.4 21.5 - - + +
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Residues in contact with CYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 3.7 22.2 - - + -
28B PHE 4.2 0.2 - - - -
29B GLN* 1.3 76.2 - - - +
31B LYS* 1.3 66.3 + - - +
34B GLY 3.9 3.1 - - - -
35B ILE* 3.8 22.2 - - - -
60B TYR* 3.7 7.0 - - - +
62B CYS* 3.7 19.7 - - - -
65B PRO* 3.3 7.3 - - - +
66B VAL* 2.9 38.5 + - + +
68B LEU* 3.8 23.6 - - - -
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLN* 3.4 46.7 - - + +
30B CYS* 1.3 83.3 + - - +
32B GLU* 1.3 69.3 + - - +
33B ASP* 3.2 19.5 - - - +
34B GLY 3.0 14.6 + - - +
36B ILE* 5.4 9.0 - - + -
60B TYR* 3.0 8.8 + - - -
62B CYS* 3.0 23.6 - - - +
65B PRO* 4.2 24.0 - - + +
66B VAL 4.6 3.2 + - - +
67B THR* 4.8 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