Contacts of the strand formed by residues 139 - 149 (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 LEU 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B SER* 4.1 9.6 - - - +
132B ALA 3.5 8.7 - - - +
133B PHE* 3.7 29.4 - - + -
137B ALA 3.9 0.8 + - - -
138B ASN* 1.3 72.4 - - - +
140B LEU* 1.3 61.3 + - - +
141B ILE* 3.5 29.4 - - - +
142B GLU* 3.7 31.2 - - + +
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Residues in contact with LEU 140 (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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39B LEU* 4.0 36.6 - - + +
42B LYS* 3.9 17.0 - - + -
43B THR* 3.4 44.4 - - - +
132B ALA* 2.9 10.0 + - + +
133B PHE* 3.7 13.2 - - - +
134B ASP* 3.7 29.2 - - + +
138B ASN* 4.4 2.0 - - + +
139B LEU* 1.3 75.9 - - - +
141B ILE* 1.3 70.0 + - + +
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Residues in contact with ILE 141 (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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30B PHE* 4.3 12.1 - - + -
33B LEU* 4.7 17.0 - - + -
34B LEU* 3.9 22.2 - - + -
37B LYS* 5.7 9.4 - - + -
39B LEU* 3.8 24.0 - - + -
131B SER* 3.2 2.9 - - - -
132B ALA* 2.9 30.5 + - + -
139B LEU* 3.5 10.4 - - - +
140B LEU* 1.3 84.5 - - + +
142B GLU* 1.3 79.6 + - + +
143B GLN* 5.8 1.1 - - - +
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Residues in contact with GLU 142 (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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30B PHE* 5.3 0.2 - - - -
129B ARG* 3.6 27.4 + - - +
130B PHE 3.2 6.1 - - - +
131B SER* 3.5 17.5 + - - +
139B LEU* 3.7 25.1 - - + +
141B ILE* 1.3 91.3 - - + +
143B GLN* 1.3 64.5 + - - +
144B VAL* 6.5 0.2 - - + -
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Residues in contact with GLN 143 (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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30B PHE* 4.4 6.7 - - + -
33B LEU* 3.9 30.3 - - + +
129B ARG* 3.4 1.8 - - - +
130B PHE* 2.8 36.7 + - - -
141B ILE* 5.8 1.0 - - - +
142B GLU* 1.3 78.1 - - - +
144B VAL* 1.3 81.3 + - - +
145B TYR* 3.5 38.4 + - + +
155B THR* 3.6 14.9 - - - +
157B GLU* 2.7 34.6 + - - +
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Residues in contact with VAL 144 (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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121B LEU* 3.5 32.5 - - + -
128B MSE 3.1 4.5 - - - +
129B ARG* 3.9 30.3 - - + +
142B GLU* 6.5 0.2 - - + -
143B GLN* 1.3 84.8 + - - +
145B TYR* 1.3 63.9 + - - +
146B TYR* 3.8 16.6 - - + -
155B THR* 3.7 1.9 - - - -
156B GLU* 3.2 50.4 + - + +
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Residues in contact with TYR 145 (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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26B ALA* 3.7 31.4 - - + -
29B ALA* 3.6 19.1 + - + +
30B PHE* 3.5 22.9 + - + -
33B LEU* 4.3 7.1 - - - +
127B GLY* 3.6 2.6 - - - -
128B MSE 2.9 41.1 + - + +
130B PHE* 3.5 31.9 - + - -
143B GLN* 3.5 31.0 - - + +
144B VAL* 1.3 77.3 - - - +
146B TYR* 1.3 66.5 + - - +
153B ILE* 4.4 13.9 - - + -
154B THR 3.4 17.0 - - - +
155B THR* 4.1 12.6 - - + -
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Residues in contact with TYR 146 (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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121B LEU* 3.3 16.2 - - + +
122B PRO* 3.3 10.2 - - - +
123B LYS* 3.0 35.6 + - + +
124B HIS* 3.3 44.2 - - + -
126B ASN 3.4 10.5 - - - +
127B GLY* 3.9 6.1 - - - -
128B MSE 4.4 2.5 - - - -
144B VAL* 3.8 9.2 - - + -
145B TYR* 1.3 74.6 - - - +
147B SER* 1.3 60.0 + - - +
148B ILE* 3.7 17.6 + - + +
153B ILE* 3.2 7.7 - - - +
154B THR* 2.9 33.6 + - + -
155B THR 4.4 1.1 - - - -
156B GLU* 3.0 42.0 + - - -
159B PHE* 3.9 13.9 - + + -
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Residues in contact with SER 147 (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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17B SER 3.9 0.2 + - - -
18B SER* 2.3 37.5 + - - +
22B GLY* 3.6 15.3 - - - -
23B PRO* 4.3 4.5 - - - -
54B LEU* 5.0 0.7 - - - -
124B HIS* 3.7 3.3 - - - -
126B ASN* 3.1 38.4 + - - +
128B MSE 3.9 19.2 - - - +
146B TYR* 1.3 68.9 - - - +
148B ILE* 1.3 60.6 + - - +
149B GLY 3.4 2.3 + - - -
151B GLY* 5.0 0.3 - - - -
152B PHE 3.7 7.8 + - - -
153B ILE* 4.2 2.0 - - - -
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Residues in contact with ILE 148 (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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124B HIS* 4.3 13.2 - - + +
146B TYR* 3.9 24.5 - - + +
147B SER* 1.3 75.4 - - - +
149B GLY* 1.3 55.7 + - - +
152B PHE* 3.1 27.9 + - + +
153B ILE 4.3 8.5 - - - +
154B THR* 3.9 22.2 - - + -
159B PHE* 4.0 14.6 - - + -
337B SER* 4.6 22.6 - - - +
340B GLU* 3.9 15.5 - - - +
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Residues in contact with GLY 149 (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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18B SER* 4.6 13.1 - - - -
147B SER* 3.4 6.1 + - - -
148B ILE* 1.3 79.4 - - - +
150B GLY* 1.3 58.8 + - - -
151B GLY 3.0 5.8 - - - -
152B PHE* 2.8 30.9 + - - +
340B GLU* 5.7 0.2 - - - -
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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