Contacts of the strand formed by residues 140 - 148 (chain F) in PDB entry 1I3R
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 140 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129F PRO* 3.2 5.5 - - - +
130F THR* 3.0 49.1 + - - +
131F LYS* 5.0 16.6 - - + +
138F HIS 4.5 2.9 - - - +
139F ASN* 1.3 78.5 - - - +
141F LEU* 1.3 61.3 + - - +
142F VAL* 3.9 0.4 - - + -
169F VAL* 5.6 0.7 - - + -
186F MET* 3.7 41.7 - - + -
187F LEU 3.0 33.7 - - - +
188F GLU* 3.4 25.4 - - + +
189F THR 4.4 1.6 - - - -
191F PRO* 5.8 1.6 - - - -
313G NAG 5.7 8.7 - - + -
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Residues in contact with LEU 141 (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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127F VAL* 4.2 3.4 - - + -
128F TYR 3.8 21.1 - - - +
129F PRO* 4.0 8.5 - - + -
140F LEU* 1.3 72.6 - - - +
142F VAL* 1.3 59.3 + - - +
157F TRP* 3.4 28.5 - - + -
186F MET* 3.3 3.0 - - - -
187F LEU* 2.8 46.5 + - + +
189F THR* 4.7 6.8 + - - +
191F PRO* 5.0 5.8 - - + +
197F TYR* 3.3 53.6 - - + -
214F TRP* 3.8 28.7 - - + -
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Residues in contact with VAL 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F THR 3.7 0.9 - - - +
127F VAL* 3.3 6.9 - - - +
128F TYR* 2.6 78.4 + - + +
130F THR* 3.7 22.0 - - + +
140F LEU* 4.6 1.6 - - + +
141F LEU* 1.3 73.0 - - - +
143F CYS* 1.3 63.6 + - - +
144F SER 4.1 1.1 - - - +
157F TRP* 3.8 2.5 - - - -
184F LEU* 3.8 21.5 - - + -
186F MET* 3.4 40.4 - - + -
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Residues in contact with CYS 143 (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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125F VAL* 3.8 20.0 - - - -
126F THR 3.7 3.4 - - - -
127F VAL* 4.5 1.1 - - - -
142F VAL* 1.3 75.3 - - - +
144F SER* 1.3 57.7 + - - +
145F VAL* 3.7 10.4 + - - +
155F VAL* 4.0 7.6 - - + -
157F TRP* 3.3 17.2 - - + +
183F THR 4.0 0.3 - - - +
184F LEU* 3.8 0.5 - - - -
185F VAL* 3.1 36.8 + - - +
199F CYS* 2.0 50.5 - - + -
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Residues in contact with SER 144 (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* 3.2 29.8 - - - +
124F THR 3.3 2.4 - - - +
125F VAL* 3.3 5.2 - - - +
126F THR* 2.8 44.9 + - - -
128F TYR* 4.0 18.2 - - - -
142F VAL* 3.7 1.8 + - - +
143F CYS* 1.3 70.6 - - - +
145F VAL* 1.3 63.6 + - - +
146F SER* 4.6 1.4 + - - -
183F THR 4.4 0.3 + - - -
184F LEU* 3.6 24.7 - - - +
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Residues in contact with VAL 145 (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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123F PRO* 3.5 18.4 - - + -
124F THR 3.7 2.7 - - - -
125F VAL* 4.5 4.7 - - + -
143F CYS* 4.0 13.5 - - - +
144F SER* 1.3 76.7 + - - +
146F SER* 1.3 59.6 + - - +
148F PHE* 3.0 12.8 - - + -
153F ILE* 3.4 29.8 - - + -
155F VAL* 4.0 14.1 - - + -
183F THR* 3.0 43.5 + - + -
185F VAL* 5.4 0.2 - - + -
201F VAL* 3.8 28.3 - - + -
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Residues in contact with SER 146 (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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94E ARG 4.8 0.9 - - - -
95E SER* 4.1 11.6 - - - -
96E PRO* 3.4 32.5 - - - +
123F PRO* 3.7 0.5 - - - +
124F THR* 3.0 41.0 + - - +
144F SER* 4.0 1.8 - - - -
145F VAL* 1.3 76.5 - - - +
147F ASP* 1.3 71.0 + - - +
148F PHE* 3.6 2.7 - - - -
181F PHE 3.8 3.1 - - - -
182F GLN* 4.1 14.4 - - - +
183F THR 5.3 0.2 - - - -
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Residues in contact with ASP 147 (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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94E ARG* 2.9 43.6 + - - +
95E SER* 5.0 5.9 - - - -
121F VAL* 3.3 25.2 - - - +
122F GLU 3.4 10.2 - - - +
124F THR* 4.7 7.9 - - - +
146F SER* 1.3 80.0 - - - +
148F PHE* 1.3 56.9 + - - +
176F ASN* 5.2 0.9 + - - +
180F THR* 4.1 18.2 + - - +
181F PHE 2.9 14.8 + - - -
182F GLN* 4.7 0.6 - - - +
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Residues in contact with PHE 148 (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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121F VAL* 3.0 10.8 - - - +
123F PRO* 3.4 27.1 - - + -
145F VAL* 3.0 47.3 - - + -
146F SER 3.9 2.7 - - - -
147F ASP* 1.3 73.6 - - - +
149F TYR* 1.3 63.6 + - - +
150F PRO 3.6 11.4 - - - -
151F GLY 3.7 19.3 - - - -
153F ILE* 3.7 16.2 - - + -
173F LEU* 3.9 7.2 - - + -
180F THR* 3.8 1.6 - - - -
181F PHE* 3.1 55.3 + - + +
182F GLN* 4.0 1.3 - - - -
183F THR* 3.8 16.2 - - + -
203F HIS* 3.6 11.4 - + - +
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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