Contacts of the strand formed by residues 45 - 51 (chain B) in PDB entry 1RGQ
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 THR 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ILE* 4.3 3.3 - - - +
39B VAL 3.3 12.1 + - - -
40B SER* 4.0 11.1 - - - -
43B THR 5.8 0.2 - - - +
44B GLN* 1.3 75.2 - - - +
46B PHE* 1.3 63.4 + - - +
112B ARG* 3.1 31.9 + - - +
140B GLY* 3.4 9.3 - - - -
194B AKP 3.3 23.7 + - - +
26C VAL* 4.7 3.2 - - - +
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Residues in contact with PHE 46 (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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38B ILE* 3.6 4.5 - - - +
39B VAL* 2.9 49.1 + - + +
40B SER* 5.0 1.3 - - - -
41B THR* 4.5 12.1 - - + -
44B GLN* 4.0 17.7 - - + -
45B THR* 1.3 76.8 + - - +
47B LEU* 1.3 78.8 + - - +
57B THR* 3.4 33.7 - - + -
58B VAL* 4.4 7.4 - - + -
61B GLY* 3.4 36.6 - - - -
62B ALA* 3.5 14.4 - - + -
112B ARG* 4.2 0.2 - - - +
140B GLY 3.4 10.5 - - - +
142B SER* 3.4 11.4 - - - +
194B AKP 4.2 26.7 - + + +
23C VAL* 5.0 3.1 - - + -
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Residues in contact with LEU 47 (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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36B VAL* 4.0 17.7 - - + -
37B GLN 3.5 2.5 - - - +
38B ILE* 4.1 23.1 - - + -
39B VAL* 3.9 2.7 - - - -
46B PHE* 1.3 91.6 - - - +
48B ALA* 1.3 54.3 + - - +
57B THR* 2.6 28.8 + - - -
110B VAL* 4.2 4.0 - - + +
111B THR 4.0 8.3 - - - +
112B ARG* 3.7 30.3 - - + +
140B GLY 3.7 9.1 + - - +
141B SER* 3.7 25.4 - - - +
142B SER 2.9 15.7 + - - +
143B GLY* 3.4 4.1 - - - -
144B GLY* 3.7 20.2 - - - +
29C ILE* 4.6 1.8 - - + -
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Residues in contact with ALA 48 (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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35B GLU 4.1 0.3 - - - +
36B VAL* 3.4 3.4 - - - +
37B GLN* 2.8 46.6 + - + +
39B VAL* 4.0 18.6 - - + -
47B LEU* 1.3 75.3 - - - +
49B THR* 1.3 62.5 + - - +
55B CYS* 3.7 22.9 - - - -
56B TRP 3.3 11.4 - - - +
57B THR* 4.1 8.1 - - - -
88B TRP* 4.8 2.7 - - + -
143B GLY 4.0 0.9 - - - -
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Residues in contact with THR 49 (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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35B GLU 3.8 7.0 - - - +
36B VAL* 4.1 3.7 - - + +
48B ALA* 1.3 74.1 + - - +
50B CYS* 1.3 64.9 + - - +
51B ILE* 3.7 19.1 + - + -
54B VAL 3.7 0.9 - - - +
56B TRP* 2.8 46.1 + - - +
97B LEU* 4.0 18.6 - - + -
143B GLY 2.7 22.9 + - - -
144B GLY* 3.7 0.7 - - - -
145B PRO* 3.5 40.7 - - + +
156B LEU* 4.6 5.4 - - - -
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Residues in contact with CYS 50 (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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35B GLU 3.0 17.1 + - - +
37B GLN* 4.7 5.4 - - - -
49B THR* 1.3 72.7 - - - +
51B ILE* 1.3 63.1 + - - +
54B VAL 3.4 5.2 - - - +
55B CYS* 4.0 27.6 - - - -
90B ALA* 4.1 7.0 - - + -
91B PRO* 4.5 2.7 - - - -
94B SER* 3.8 27.4 - - - +
95B ARG 3.6 18.2 - - - +
96B SER* 3.5 11.9 - - - +
97B LEU* 2.9 28.1 + - - +
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Residues in contact with ILE 51 (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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49B THR* 3.7 20.3 + - + -
50B CYS* 1.3 79.2 - - - +
52B ASN* 1.3 84.1 + - - +
53B GLY 3.5 1.6 - - - -
54B VAL* 3.1 11.3 + - - +
56B TRP* 3.1 27.2 + - + -
97B LEU* 3.5 17.7 - - + +
99B PRO* 4.1 13.9 - - + -
145B PRO* 5.9 1.1 - - + -
153B ALA* 4.1 24.2 - - + -
156B LEU* 3.7 29.4 - - + -
175B VAL* 4.8 4.7 - - + -
178B LEU* 3.9 19.7 - - + -
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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