Contacts of the strand formed by residues 90 - 96 (chain D) in PDB entry 1RG9
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 ALA 90 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A THR* 3.9 8.7 - - - +
48A GLY* 3.7 21.2 - - - +
49A MET* 4.0 13.9 - - + -
48D GLY 2.6 18.9 + - - +
49D MET* 3.3 13.4 - - + -
50D VAL* 2.9 26.8 + - - +
89D CYS* 1.3 76.4 - - - +
91D VAL* 1.3 63.3 + - - +
92D LEU* 4.0 11.0 - - + -
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Residues in contact with VAL 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A THR* 4.9 1.0 + - - -
93B SER 3.6 9.4 - - - +
94B ALA* 3.9 9.6 - - - +
95B ILE 5.0 0.7 + - - -
50D VAL* 3.6 5.6 - - + +
52D VAL* 4.9 1.3 - - + -
64D ILE* 4.6 6.5 - - + -
65D GLU* 3.9 29.6 - - + +
68D THR* 4.0 25.6 - - + +
69D ARG* 3.5 45.8 - - + +
89D CYS* 3.9 4.5 + - - -
90D ALA* 1.3 79.0 - - - +
92D LEU* 1.3 70.0 + - - +
93D SER* 5.1 1.2 + - - +
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A MET* 3.6 38.1 - - + -
92A LEU* 6.1 6.1 - - + -
51B LEU* 4.7 11.2 - - + -
92B LEU* 3.8 23.3 - - + -
93B SER 3.5 10.1 - - - +
94B ALA* 4.4 6.5 - - + -
49D MET* 4.9 12.8 - - + -
50D VAL 2.7 13.5 + - - +
51D LEU* 3.8 20.9 - - + -
52D VAL* 2.8 27.7 + - - +
90D ALA* 4.0 14.1 - - + -
91D VAL* 1.3 80.8 - - - +
93D SER* 1.3 64.9 + - - +
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Residues in contact with SER 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B VAL 3.7 1.2 - - - +
92B LEU* 3.3 8.0 - - - -
93B SER* 3.0 44.3 + - - +
51D LEU* 4.5 1.1 - - - -
52D VAL 3.1 8.1 + - - -
64D ILE* 3.6 31.3 - - - +
91D VAL* 5.1 1.9 + - - +
92D LEU* 1.3 79.9 + - - +
94D ALA* 1.3 60.0 + - - +
95D ILE* 3.8 10.9 - - - +
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B VAL 3.8 9.6 - - - +
92B LEU* 4.1 13.5 - - + -
44C TYR* 5.5 0.9 - - + -
46C LYS* 4.2 13.6 - - + +
47C THR* 6.1 0.9 - - - +
49C MET* 4.0 27.8 - - + -
51D LEU* 4.2 6.2 - - + +
52D VAL 2.9 7.9 + - - -
53D GLY* 3.0 17.1 - - - -
54D GLY 3.1 8.7 + - - +
93D SER* 1.3 73.0 - - - +
95D ILE* 1.3 60.9 + - - +
96D GLY 4.0 0.6 + - - -
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Residues in contact with ILE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLU* 4.1 13.3 - - - +
91B VAL 4.9 1.2 + - - -
26D VAL* 6.0 0.2 - - + -
52D VAL* 3.5 30.1 - - + +
53D GLY* 3.8 9.9 - - - +
54D GLY 3.4 6.3 - - - +
56D ILE* 3.7 37.9 - - + +
64D ILE* 4.2 31.4 - - + -
93D SER* 3.8 10.5 - - - +
94D ALA* 1.3 72.5 - - - +
96D GLY* 1.3 72.3 + - - +
97D LYS* 5.7 1.2 + - - -
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Residues in contact with GLY 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLU* 3.3 18.4 - - - -
46C LYS* 4.7 8.9 - - - +
47C THR* 5.8 4.0 - - - +
54D GLY 2.8 11.4 + - - -
55D GLU* 3.8 3.4 - - - -
56D ILE 2.6 34.6 + - - +
94D ALA 4.0 1.2 + - - -
95D ILE* 1.3 77.8 - - - +
97D LYS* 1.3 57.9 + - - -
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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