Contacts of the strand formed by residues 45 - 51 (chain A) in PDB entry 4RQO
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 ARG 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A THR* 3.8 1.4 - - - +
44A GLN* 1.3 80.2 - - + +
46A VAL* 1.3 67.7 + - - +
47A LYS* 3.9 14.1 - - - +
105A ILE* 3.8 5.3 - - - +
106A PRO 4.9 3.1 - - - +
111A THR* 3.1 30.4 + - - +
112A ASP* 2.8 36.7 + - - +
132A ALA* 3.2 4.9 - - - +
133A PHE* 2.7 81.9 + - + +
134A ASP 5.3 2.0 - - - +
137A ALA* 5.9 5.7 - - - +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 4.5 13.7 - - + -
34A LEU* 4.9 1.1 - - + -
43A THR* 4.0 15.7 - - + -
45A ARG* 1.3 79.4 - - - +
47A LYS* 1.3 71.2 + - - +
48A VAL* 4.5 2.5 - - + -
71A LEU* 3.9 29.8 - - + -
97A LEU* 4.6 7.6 - - + -
99A LEU* 3.8 25.6 - - + -
105A ILE* 3.6 12.4 - - + +
106A PRO 5.4 0.2 + - - -
107A PHE* 4.1 7.7 - - + -
112A ASP* 3.4 24.0 - - - +
130A PHE* 4.8 2.2 - - + -
131A SER 3.3 10.5 - - - +
132A ALA* 4.5 5.6 - - + -
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG* 3.9 16.3 - - - +
46A VAL* 1.3 75.4 - - - +
48A VAL* 1.3 68.3 + - - +
49A GLU* 3.8 29.9 + - + +
111A THR 3.6 24.9 - - - +
112A ASP* 3.6 6.3 - - - +
114A LEU* 3.9 20.2 - - - +
129A ARG 3.5 1.2 - - - +
130A PHE* 3.4 6.1 - - - -
131A SER* 2.8 37.8 + - - +
133A PHE* 3.7 30.3 - - + -
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 4.5 2.0 - - + -
47A LYS* 1.3 79.6 - - - +
49A GLU* 1.3 62.3 + - - +
50A LEU* 4.2 11.2 - - + -
67A ILE* 3.8 46.7 - - + -
71A LEU* 4.1 17.0 - - + -
107A PHE* 5.4 2.2 - - + -
112A ASP 2.9 12.5 + - - +
113A PHE* 3.4 20.7 + - + -
114A LEU* 2.8 32.3 + - - +
128A MSE 5.3 0.7 - - + -
129A ARG 3.6 6.7 - - - +
130A PHE* 4.1 16.6 - - + -
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.8 34.4 + - + +
48A VAL* 1.3 78.3 - - - +
50A LEU* 1.3 63.9 + - - +
51A TYR* 3.5 26.6 + - + -
114A LEU* 3.5 13.1 - - + +
116A LEU* 3.8 22.8 - - + +
128A MSE 3.4 8.0 - - - +
129A ARG* 3.1 58.1 + - - +
131A SER* 4.3 5.7 + - - -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 4.2 3.6 - - + -
49A GLU* 1.3 76.1 - - - +
51A TYR* 1.3 59.5 + - - +
54A LEU* 4.2 11.0 - - + +
55A ALA* 3.5 15.7 - - + +
63A THR* 3.8 24.7 - - + -
67A ILE* 3.5 28.3 - - + -
113A PHE* 3.7 24.9 - - + -
114A LEU 2.7 15.2 + - - +
115A PHE* 3.9 22.7 - - + -
116A LEU* 2.8 33.3 + - - +
127A GLY 4.2 1.6 - - - -
128A MSE 3.9 18.4 - - + -
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 3.5 37.1 + - + -
50A LEU* 1.3 73.1 - - - +
52A GLY* 1.3 67.1 + - - +
54A LEU* 3.1 21.3 + - - +
55A ALA* 3.9 2.0 - - - -
116A LEU* 3.6 20.2 - - + +
119A GLU* 3.4 46.1 + - + +
120A LEU 4.6 2.0 - - - -
121A LEU* 3.3 49.8 - - + +
125A SER 3.4 6.9 - - - +
127A GLY* 3.0 20.7 + - - +
128A MSE 4.5 0.4 - - - -
129A ARG* 3.4 29.7 + - + -
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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