Contacts of the strand formed by residues 46 - 52 (chain H) in PDB entry 2PGW
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 46 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10H ARG* 4.2 12.8 - - - +
38H GLU* 4.1 14.8 - - + -
39H ILE 3.3 15.7 - - - +
40H GLU* 3.8 15.3 - - + -
44H GLY 3.4 12.3 + - - +
45H THR* 1.3 83.7 - - - +
47H GLY* 1.3 71.5 + - - +
48H ILE* 4.1 11.2 - - + +
116H LEU* 4.1 4.0 - - - -
119H LYS* 2.8 31.5 + - - +
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Residues in contact with GLY 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H ILE 3.7 0.9 - - - +
38H GLU* 3.4 4.5 - - - -
39H ILE* 2.8 35.8 + - - -
46H VAL* 1.3 73.2 - - - +
48H ILE* 1.3 62.1 + - - +
112H ALA* 3.3 24.2 - - - +
115H ASP* 3.2 7.6 - - - -
116H LEU* 3.8 13.3 - - - +
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Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H LEU* 5.1 4.5 - - + -
37H ILE 3.6 4.7 - - - +
38H GLU* 4.2 18.2 - - + +
46H VAL* 4.1 16.8 - - + +
47H GLY* 1.3 80.1 - - - +
49H GLY* 1.3 66.6 + - - +
112H ALA* 3.8 7.3 - - - -
115H ASP* 2.8 12.3 + - - +
119H LYS* 4.5 10.1 - - - +
305H ILE* 3.9 17.3 - - + -
356H LEU* 3.8 14.6 - - - +
358H PHE* 3.6 27.9 - - + -
360H LEU* 3.5 38.4 - - + -
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Residues in contact with GLY 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H LEU* 3.4 7.8 - - - +
37H ILE* 2.9 32.7 + - - +
48H ILE* 1.3 76.6 - - - +
50H GLU* 1.3 63.8 + - - +
108H GLY 3.8 6.7 - - - -
111H MSE 3.4 20.9 - - - -
112H ALA* 3.7 1.4 - - - +
305H ILE* 4.0 9.2 - - - -
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Residues in contact with GLU 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H VAL* 3.9 8.1 - - + +
35H ASN 3.3 9.0 - - - +
36H LEU* 3.7 16.7 - - + +
37H ILE* 4.3 1.1 - - - -
49H GLY* 1.3 74.7 - - - +
51H CYS* 1.3 64.1 + - - +
107H SER* 5.0 1.0 + - - -
108H GLY* 3.3 17.1 + - - -
111H MSE 3.8 14.2 - - - +
302H THR* 3.1 8.4 - - + +
303H THR* 2.6 52.3 + - - +
305H ILE* 3.6 19.6 - - + +
306H THR* 2.6 31.8 + - - +
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Residues in contact with CYS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H VAL* 3.5 8.3 - - - +
35H ASN* 3.0 34.5 + - + +
37H ILE* 5.1 0.4 - - - -
50H GLU* 1.3 73.2 - - - +
52H THR* 1.3 70.8 + - - +
64H LEU* 3.9 25.8 - - + -
104H GLN 3.6 15.5 - - - +
105H ILE* 3.1 37.9 - - + -
107H SER* 5.9 0.7 - - - -
108H GLY* 3.7 15.0 - - - -
302H THR* 5.0 3.4 - - - -
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Residues in contact with THR 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C HIS 5.6 2.2 - - - +
33H ALA 4.7 5.2 - - - -
35H ASN* 4.8 0.7 - - - +
51H CYS* 1.3 86.3 - - - +
53H VAL* 1.3 62.1 + - - +
54H ALA* 4.9 2.5 - - - -
60H THR* 4.5 3.6 + - - -
104H GLN* 3.2 39.5 + - - +
105H ILE* 5.2 1.0 - - - +
273H ARG* 3.6 36.1 + - + +
300H SER* 4.0 8.7 - - - +
301H PHE* 4.8 6.3 - - + +
302H THR* 3.7 25.8 - - + -
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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