Contacts of the strand formed by residues 155 - 162 (chain F) in PDB entry 1R5I
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 PHE 155 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E ASP 5.3 1.8 - - - -
29E ASP* 4.4 2.0 - - - -
121F GLY 3.0 24.3 + - - -
122F PHE* 2.8 44.1 + - + -
123F TYR* 3.8 24.2 - + - -
124F PRO 4.0 0.4 - - - -
125F GLY* 3.4 34.3 - - - -
147F LEU* 3.6 26.2 - - + -
148F ILE 3.1 17.3 - - - +
149F GLN* 3.4 43.3 - - + -
150F ASN* 3.5 4.7 + - - +
154F THR* 1.3 75.8 - - - +
156F GLN* 1.3 62.4 + - - +
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Residues in contact with GLN 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E LEU* 4.9 9.7 - - - +
93E THR* 3.1 27.5 + - - +
94E ASN* 3.4 14.4 + - - +
95E SER* 5.4 2.2 - - - +
106E ILE* 4.6 0.9 - - - +
108E PHE* 5.5 0.8 - - - -
119F VAL 3.2 14.6 - - - +
120F SER* 3.9 12.5 - - - -
122F PHE* 3.8 2.7 - - - -
147F LEU* 3.9 1.6 - - - +
148F ILE* 2.9 53.4 + - + +
150F ASN* 2.9 26.2 - - - +
155F PHE* 1.3 77.9 - - - +
157F THR* 1.3 66.9 + - - +
158F LEU* 4.9 15.1 - - + +
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Residues in contact with THR 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F CYS 3.7 1.2 - - - +
119F VAL* 2.9 47.5 + - + +
122F PHE* 4.0 14.1 - - + -
127F ILE* 4.8 9.6 - - + -
129F VAL* 4.9 7.2 - - + -
144F SER* 3.3 13.2 + - - -
145F THR* 3.7 7.4 - - - -
146F GLY 3.1 20.4 + - - -
147F LEU* 4.4 4.5 - - + -
148F ILE* 5.2 0.4 - - - -
156F GLN* 1.3 82.7 - - - +
158F LEU* 1.3 70.6 + - - +
159F VAL* 4.1 4.1 - - + +
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Residues in contact with LEU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E PRO* 6.1 1.3 - - + -
102F TYR* 3.9 19.5 - - - +
116F VAL* 4.0 14.1 - - + -
117F CYS 3.5 2.2 - - - -
118F SER* 3.9 26.2 - - - +
119F VAL 4.6 0.7 - - - +
143F VAL 4.0 0.2 - - - +
144F SER* 2.8 21.2 + - - -
145F THR* 3.0 36.0 + - + -
156F GLN* 4.9 14.1 - - + +
157F THR* 1.3 88.8 + - - +
159F VAL* 1.3 62.0 + - - +
160F MET* 4.0 10.5 - - + +
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Residues in contact with VAL 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F CYS* 2.9 32.4 + - + +
119F VAL* 5.5 0.2 - - + -
129F VAL* 3.5 48.9 - - + +
131F TRP* 3.1 27.1 + - + -
142F VAL* 4.6 11.2 - - + -
143F VAL 3.6 6.3 - - - +
144F SER* 3.8 15.9 - - - +
157F THR* 4.1 9.2 - - + +
158F LEU* 1.3 77.0 - - - +
160F MET* 1.3 63.3 - - - +
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Residues in contact with MET 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F SER* 5.7 2.2 - - - +
114F LEU* 3.5 31.4 - - + -
115F LEU 3.2 4.3 - - - +
116F VAL* 3.6 40.8 - - + -
131F TRP* 3.6 2.7 - - - -
141F GLY 3.7 0.3 - - - +
142F VAL* 3.1 8.5 - - - +
143F VAL* 2.7 52.7 + - + +
144F SER* 5.2 1.1 - - - -
145F THR* 5.0 5.6 - - - -
158F LEU* 4.2 20.4 - - + +
159F VAL* 1.3 72.7 - - - +
161F LEU* 1.3 61.6 + - - +
162F GLU* 4.2 0.4 - - - -
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Residues in contact with LEU 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F LEU* 2.9 24.5 - - - +
115F LEU* 2.9 17.5 + - + +
131F TRP* 3.5 41.0 - - + +
132F PHE 5.5 0.2 - - - +
138F GLU* 4.0 21.1 - - + -
141F GLY* 3.6 10.3 - - - -
142F VAL* 3.8 23.3 - - + -
160F MET* 1.3 72.4 - - - +
162F GLU* 1.3 59.5 + - - +
163F THR* 3.0 39.3 + - + +
171F TYR* 4.0 20.9 - - + -
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Residues in contact with GLU 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F THR* 5.3 5.2 - - - +
113F ASN* 4.6 2.0 - - + -
114F LEU* 3.9 18.8 - - + +
140F ALA 4.9 1.9 - - - +
141F GLY* 2.8 35.4 + - - +
143F VAL* 3.2 26.3 - - + +
161F LEU* 1.3 68.4 - - - +
163F THR* 1.3 69.0 + - - +
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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