Contacts of the strand formed by residues 45 - 51 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B THR* 3.7 2.7 - - - +
44B GLN* 1.3 81.8 - - - +
46B VAL* 1.3 69.9 + - - +
47B LYS* 3.7 15.5 - - - +
105B ILE* 3.8 7.0 - - - +
106B PRO 4.5 5.4 - - - +
111B THR* 3.1 40.5 + - - +
112B ASP* 2.7 26.6 + - - +
132B ALA* 3.3 4.0 - - - -
133B PHE* 2.9 77.6 + - + +
134B ASP 5.1 2.7 - - - +
137B ALA* 6.0 4.1 - - - +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 4.0 24.0 - - + -
34B LEU* 5.1 0.7 - - + -
43B THR* 4.2 13.9 - - + -
45B ARG* 1.3 82.3 - - - +
47B LYS* 1.3 70.4 + - - +
48B VAL* 4.5 2.9 - - + -
71B LEU* 4.1 25.4 - - + -
97B LEU* 4.9 4.9 - - + -
99B LEU* 3.7 29.4 - - + -
105B ILE* 4.0 9.8 - - + +
106B PRO 5.1 0.8 + - - -
107B PHE* 4.1 8.1 - - + -
112B ASP* 3.4 25.7 - - - +
130B PHE* 4.8 0.4 - - + -
131B SER 3.2 11.7 - - - +
132B ALA* 4.7 0.2 - - + -
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Residues in contact with LYS 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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45B ARG* 3.7 18.3 - - - +
46B VAL* 1.3 78.2 - - - +
48B VAL* 1.3 71.4 + - - +
49B GLU* 3.7 32.5 + - + +
111B THR 3.6 22.0 + - - +
112B ASP* 3.4 6.7 - - - +
114B LEU* 4.0 14.7 - - + +
129B ARG 3.7 0.9 - - - +
130B PHE* 3.4 4.5 - - - -
131B SER* 2.7 40.2 + - - +
133B PHE* 3.8 27.3 - - + -
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Residues in contact with VAL 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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46B VAL* 4.5 2.2 - - + -
47B LYS* 1.3 79.2 - - - +
49B GLU* 1.3 68.3 + - - +
50B LEU* 4.1 10.1 - - + -
67B ILE* 4.0 29.2 - - + -
71B LEU* 4.0 13.9 - - + -
107B PHE* 5.5 2.0 - - + -
112B ASP 2.6 12.8 + - - +
113B PHE* 3.4 33.6 + - + -
114B LEU* 2.9 26.9 + - - +
128B MSE 5.5 0.4 - - + -
129B ARG 3.6 4.5 - - - +
130B PHE* 3.8 29.6 - - + -
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Residues in contact with GLU 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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47B LYS* 3.7 34.2 + - + +
48B VAL* 1.3 78.9 - - - +
50B LEU* 1.3 64.3 + - - +
51B TYR* 3.7 20.4 + - + -
114B LEU* 3.6 20.3 - - + +
116B LEU* 4.2 9.0 - - + +
128B MSE 3.1 6.2 - - - +
129B ARG* 2.8 80.7 + - + +
131B SER* 4.4 5.2 + - - -
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Residues in contact with LEU 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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48B VAL* 4.1 5.8 - - + -
49B GLU* 1.3 75.5 - - - +
51B TYR* 1.3 59.9 + - - +
54B LEU* 4.2 15.3 - - + +
55B ALA* 3.3 15.7 - - + +
63B THR* 3.6 26.0 - - + -
67B ILE* 3.7 25.8 - - + -
113B PHE* 3.9 24.7 - - + -
114B LEU 3.0 14.1 + - - +
115B PHE* 4.0 18.6 - - + -
116B LEU* 2.8 34.3 + - - +
127B GLY 3.8 2.0 - - - -
128B MSE 3.8 17.9 - - + -
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Residues in contact with TYR 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 GLU* 3.7 29.3 + - + -
50B LEU* 1.3 78.1 - - - +
52B GLY* 1.3 68.5 + - - +
53B SER 3.3 0.3 + - - -
54B LEU* 3.0 20.1 + - - +
55B ALA* 3.1 3.4 + - - -
116B LEU* 3.6 27.4 - - + +
119B GLU* 3.7 40.3 + - + +
120B LEU 4.0 4.0 - - - -
121B LEU* 3.6 50.3 - - + +
125B SER 3.5 6.0 - - - +
127B GLY* 2.8 15.6 + - - +
129B ARG* 2.9 30.8 + - + -
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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