Contacts of the strand formed by residues 149 - 155 (chain A) in PDB entry 3C6M
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 ASN 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ASP* 3.0 22.4 + - - -
143A GLU 3.3 10.4 + - - -
144A ASP* 2.7 28.6 + - - +
148A GLN* 1.3 75.1 - - - +
150A ILE* 1.3 61.0 + - - +
151A LYS* 3.0 33.6 + - - +
163A ILE 3.7 0.2 - - - +
164A LEU* 3.5 6.6 - - - +
165A SER* 3.0 39.1 + - - +
166A GLY 5.0 1.2 + - - -
107B ARG* 4.3 4.6 - - - +
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A TYR* 3.8 25.5 - - + +
142A ASP* 3.3 4.7 - - - +
143A GLU 2.8 35.4 + - - +
145A SER* 3.8 9.2 - - - +
148A GLN* 3.9 11.2 - - + +
149A ASN* 1.3 76.9 - - - +
151A LYS* 1.3 61.0 + - - +
152A ILE* 4.9 1.8 - - + -
162A LEU* 4.1 15.5 - - + -
163A ILE 3.8 2.0 - - - -
164A LEU* 3.8 21.8 - - + -
222A ASP* 3.6 13.0 - - - +
224A MET* 3.7 25.4 - - + +
225A VAL* 3.6 26.9 - - + +
228A GLY* 6.0 0.9 - - - -
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASP* 5.7 2.2 - - - -
124A TRP* 3.7 36.1 - - + -
141A TYR 3.3 2.5 - - - +
142A ASP* 3.3 21.2 + - + +
149A ASN* 3.0 24.8 + - - +
150A ILE* 1.3 71.4 - - - +
152A ILE* 1.3 69.2 + - - +
153A LEU* 4.1 18.6 - - + -
161A ILE 4.2 0.2 - - - -
162A LEU* 3.5 2.9 - - - +
163A ILE* 2.8 51.5 + - + +
166A GLY 5.5 2.0 - - - +
107B ARG* 3.1 43.2 - - - +
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Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 2.8 38.2 + - + +
141A TYR* 2.7 32.6 + - + +
150A ILE* 4.9 1.1 - - + -
151A LYS* 1.3 79.5 - - - +
153A LEU* 1.3 57.3 + - - +
160A ASN* 3.8 29.2 - - + -
161A ILE 3.4 6.3 - - - +
162A LEU* 3.8 21.1 - - + -
228A GLY* 3.6 36.8 - - - +
229A CYS 4.2 1.1 - - - +
232A TYR* 3.8 23.1 - - + -
233A MET* 4.2 11.4 - - + -
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ILE* 5.8 0.2 - - + -
121A ASP* 3.7 12.8 - - + +
124A TRP* 3.5 37.2 - - + +
136A ILE* 3.7 21.5 - - + -
138A GLU 3.5 2.2 - - - +
139A VAL* 3.9 34.8 - - + -
151A LYS* 4.3 18.8 - - + -
152A ILE* 1.3 82.2 - - - +
154A HIS* 1.3 61.9 + - - +
155A SER 3.7 0.9 + - - -
160A ASN* 3.4 3.3 - - - -
161A ILE* 2.8 35.5 + - + +
163A ILE* 3.7 19.3 - - + -
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Residues in contact with HIS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 3.0 6.8 - - - -
137A ASP* 2.5 67.5 + - - +
138A GLU* 2.9 29.4 + - + +
140A VAL* 4.1 4.4 - - + +
153A LEU* 1.3 73.3 - - - +
155A SER* 1.3 78.8 + - - +
156A LYS* 4.0 5.7 + - - +
159A GLY* 4.1 3.3 - - - -
160A ASN* 3.3 24.8 + - - +
327C LEU* 4.1 18.2 - - + +
330C GLU* 2.7 39.3 + - - -
334C ARG* 4.9 0.2 + - - -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ASP* 2.7 31.1 + - - -
136A ILE* 4.0 3.4 - - - -
153A LEU 3.7 0.4 + - - -
154A HIS* 1.3 82.1 - - - +
156A LYS* 1.3 57.9 + - - +
158A PHE* 2.8 24.6 + - - -
159A GLY* 2.9 41.1 + - - +
161A ILE* 3.7 23.6 - - - -
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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