Contacts of the strand formed by residues 42 - 50 (chain D) in PDB entry 1RRP
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 CYS 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D GLU* 3.4 27.1 - - + +
41D PHE* 1.3 82.4 - - - +
43D ASN* 1.3 61.8 + - - +
64D ASN* 4.2 19.3 - - - -
65D VAL 3.4 7.2 - - - -
66D LYS* 3.9 21.8 - - + -
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Residues in contact with ASN 43 (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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41D PHE* 3.4 24.2 - - + -
42D CYS* 1.3 75.4 - - - +
44D ARG* 1.3 87.4 + - - +
64D ASN* 3.6 5.6 - - - -
65D VAL* 2.7 43.6 + - - +
131D PHE* 4.6 5.8 - - + -
136D GLU* 3.2 47.1 + - - +
139D LEU* 5.6 5.6 - - + +
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Residues in contact with ARG 44 (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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43D ASN* 1.3 96.4 + - - +
45D ALA* 1.3 65.1 + - - +
62D ILE* 3.9 21.9 - - - +
63D GLY* 2.7 15.5 + - - +
64D ASN* 2.9 18.8 + - - +
83D GLU* 2.6 39.2 + - - -
131D PHE* 4.0 4.7 - - - -
132D LYS* 4.5 22.8 + - - +
136D GLU* 4.7 2.6 - - - +
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Residues in contact with ALA 45 (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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43D ASN 3.8 0.6 + - - -
44D ARG* 1.3 80.0 - - - +
46D LYS* 1.3 61.9 + - - +
62D ILE* 3.3 8.2 - - - +
63D GLY 2.5 33.1 + - - -
65D VAL* 4.4 3.6 - - + -
80D MET* 3.0 8.1 - - + +
129D ILE* 4.0 15.5 - - + -
130D ARG 3.4 13.7 - - - +
131D PHE* 3.3 29.6 - - + +
132D LYS 6.0 0.2 - - - +
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Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D ALA* 1.3 74.8 - - - +
47D LEU* 1.3 60.0 + - - +
48D PHE* 3.2 32.5 - - + -
59D GLU* 3.7 32.1 + - + +
61D GLY 3.2 15.0 - - - +
62D ILE* 3.3 22.0 - - + -
129D ILE* 3.5 6.2 - - - +
130D ARG* 2.9 54.8 + - + +
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Residues in contact with LEU 47 (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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46D LYS* 1.3 72.7 - - - +
48D PHE* 1.3 70.3 + - - +
59D GLU* 3.6 3.1 - - - +
60D ARG* 2.5 41.0 + - + -
61D GLY* 2.5 21.9 + - - +
80D MET* 3.6 25.3 - - - +
89D CYS* 2.8 33.4 - - - +
90D ALA* 4.0 8.3 - - + -
112D TRP* 4.0 16.2 - - + -
127D LEU* 4.4 11.9 - - + -
128D ALA 3.0 22.2 - - - +
129D ILE* 3.6 14.6 - - + -
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Residues in contact with PHE 48 (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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46D LYS* 3.2 55.4 - - + -
47D LEU* 1.3 77.9 - - - +
49D ARG* 1.3 60.3 + - - +
57D TRP* 3.2 28.3 - + + -
58D LYS 3.2 16.4 - - - +
59D GLU* 4.0 15.7 - - + -
60D ARG* 4.0 2.0 - - - +
127D LEU* 3.3 10.3 - - - +
128D ALA* 2.6 56.1 + - + +
130D ARG* 3.7 33.4 - - + -
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Residues in contact with ARG 49 (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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31C LEU 5.8 0.2 + - - -
32C THR* 3.6 30.5 + - - +
48D PHE* 1.3 72.8 - - - +
50D PHE* 1.3 84.9 + - - +
51D ASP* 6.1 0.4 - - - +
57D TRP* 3.1 4.7 - - - -
58D LYS* 2.9 42.9 + - - +
60D ARG* 3.8 39.5 - - + +
119D ASP* 5.1 2.0 + - - -
123D LYS* 5.7 3.6 - - - +
125D GLU* 3.6 48.8 + - + +
126D GLN 3.7 2.2 - - - +
127D LEU* 3.9 6.7 - - + -
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Residues in contact with PHE 50 (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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49D ARG* 1.3 96.9 + - - +
51D ASP* 1.3 72.7 + - - +
52D VAL* 3.0 44.1 - - + +
55D LYS* 3.1 41.5 - - + -
56D GLU 4.4 1.1 - - - -
57D TRP* 2.9 53.9 - + + -
58D LYS* 5.6 0.2 - - - -
126D GLN* 3.2 25.5 + - + +
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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