Contacts of the strand formed by residues 143 - 149 (chain F) in PDB entry 2I9B
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 HIS 143 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F GLY* 3.5 0.5 - - - -
100F SER* 2.6 39.5 + - - +
105F CYS* 3.9 23.3 - - + -
124F ASP* 5.1 3.8 + - - +
125F VAL 3.6 2.9 - - - -
126F VAL* 3.5 23.2 - - + +
141F ASP* 4.0 0.6 - - - +
142F ARG* 1.3 100.3 - - + +
144F LEU* 1.3 70.2 + - - +
145F ARG* 6.3 0.4 - - + -
181F ILE* 3.5 26.0 - - + +
182F LEU 3.4 17.1 + - - -
183F GLU* 2.9 41.2 + - - -
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Residues in contact with LEU 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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22B ASN* 3.8 25.1 - - - +
55F LEU* 4.0 12.8 - - + -
57F TYR* 3.8 41.3 - - + +
98F CYS 3.5 3.1 - - - -
99F GLY* 4.0 6.7 - - - -
105F CYS* 4.6 0.4 - - - -
123F LEU 3.9 0.3 - - - +
124F ASP* 3.4 1.0 - - - +
125F VAL* 2.8 49.4 + - + +
140F ASP* 5.1 4.7 - - - +
141F ASP* 3.6 33.2 - - + +
143F HIS* 1.3 86.5 - - - +
145F ARG* 1.3 67.9 + - - +
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Residues in contact with ARG 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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55F LEU* 5.8 1.1 - - - -
57F TYR* 3.4 9.4 - - - +
96F ILE* 3.8 15.1 - - - +
97F SER* 2.7 27.5 + - - -
98F CYS* 2.8 39.3 + - - +
105F CYS* 4.8 1.6 - - - -
110F HIS* 3.3 26.7 + - - -
123F LEU 3.1 12.1 - - - +
124F ASP* 3.0 29.9 + - - +
143F HIS* 6.3 0.4 - - + -
144F LEU* 1.3 82.2 - - - +
146F GLY* 1.3 53.9 + - - +
177F ASN* 3.4 23.4 + - - +
178F GLU* 4.1 3.2 + - - +
179F GLY* 2.9 39.4 + - - +
180F PRO 3.5 14.3 + - - -
181F ILE* 4.0 10.9 - - - +
182F LEU* 4.9 0.4 - - - +
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Residues in contact with GLY 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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55F LEU* 5.3 2.2 - - - +
56F SER 3.4 12.1 - - - -
57F TYR* 4.7 0.2 - - - -
95F CYS* 3.9 3.0 - - - +
96F ILE 3.8 8.3 - - - -
97F SER* 3.9 6.1 - - - -
113F LEU* 4.4 1.8 - - - -
122F CYS* 3.3 5.4 - - - -
123F LEU* 2.6 45.2 + - - +
145F ARG* 1.3 75.0 - - - +
147F CYS* 1.3 61.9 + - - -
177F ASN* 3.5 4.6 + - - +
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Residues in contact with CYS 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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55F LEU* 3.4 2.4 - - - +
56F SER* 2.8 41.8 + - - +
95F CYS* 4.0 3.6 - - - -
113F LEU* 3.7 26.0 - - + +
115F CYS* 2.0 57.7 - - + -
120F GLU* 3.5 11.6 - - - +
121F GLN 3.3 5.8 - - - -
123F LEU* 3.8 5.0 - - - +
146F GLY* 1.3 73.1 - - - -
148F GLY* 1.3 57.9 - - - +
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Residues in contact with GLY 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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54F THR* 2.9 15.3 - - - -
120F GLU* 3.4 19.1 + - - +
121F GLN* 2.7 40.0 + - - +
123F LEU* 3.7 12.2 - - - +
147F CYS* 1.3 76.7 - - - +
149F TYR* 1.3 60.8 + - - -
153F CYS* 4.9 0.2 - - - -
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Residues in contact with TYR 149 (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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52F ASN 4.4 13.7 - - - -
53F ARG* 3.2 10.4 - - - +
54F THR* 2.7 36.6 + - + +
119F GLU* 3.3 47.1 - - + +
121F GLN* 4.4 10.8 - - + -
148F GLY* 1.3 74.8 - - - +
150F LEU* 1.3 69.8 + - - +
151F PRO* 5.2 2.1 + - + -
153F CYS* 3.5 39.6 + - + -
154F PRO* 5.3 1.7 - - + +
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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