Contacts of the strand formed by residues 146 - 151 (chain A) in PDB entry 3M6L
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 ILE 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ARG* 3.3 14.4 - - + +
62A VAL* 4.9 1.3 - - + -
123A ALA* 3.6 38.4 - - + +
126A PHE* 3.9 15.7 - - + -
127A ALA* 3.6 23.3 - - + +
130A ALA* 4.1 0.4 - - + -
144A HIS* 3.8 19.7 - - + +
145A LYS* 1.3 81.8 - - - +
147A TYR* 1.3 64.3 + - - +
174A ASN* 2.8 43.3 + - + +
175A PHE* 3.6 6.9 - - + -
176A ILE* 2.9 29.6 + - - +
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Residues in contact with TYR 147 (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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42A LEU* 3.7 31.0 - - + -
45A HIS* 4.1 8.2 + - + +
46A LEU* 3.7 25.1 - - + -
59A ASP* 3.6 26.2 + - + -
60A ARG 2.8 8.9 + - - +
61A LEU* 3.5 16.1 - - + +
62A VAL* 2.8 27.5 + - - +
145A LYS* 3.7 17.8 - - + +
146A ILE* 1.3 76.2 - - - +
148A CYS* 1.3 61.4 + - - +
149A LEU 4.3 0.2 - - - -
176A ILE* 3.3 38.6 - - + -
178A ILE* 4.6 5.8 - - + -
224A LEU* 4.1 11.0 - - + -
228A LYS* 3.6 30.7 - - - +
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Residues in contact with CYS 148 (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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62A VAL* 3.2 10.8 - - + -
64A SER* 4.0 9.2 - - - -
119A GLY 3.9 21.3 - - - -
120A VAL* 4.0 10.8 - - - -
123A ALA* 3.6 17.5 - - + -
147A TYR* 1.3 75.3 - - - +
149A LEU* 1.3 71.1 + - - +
175A PHE* 4.1 3.4 - - + -
176A ILE 2.9 7.3 + - - -
177A LEU* 3.6 25.5 - - + +
178A ILE* 2.7 34.0 + - - +
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Residues in contact with LEU 149 (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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35A LEU* 4.5 29.8 - - + +
38A ILE* 4.3 10.8 - - + -
39A LEU* 4.9 11.7 - - + -
42A LEU* 4.5 7.2 - - + -
61A LEU* 4.6 9.2 - - + -
62A VAL 2.9 12.3 + - - +
63A PHE* 3.7 41.0 - - + -
64A SER* 2.8 28.4 + - - -
65A GLY 3.8 2.5 + - - -
71A LEU* 5.3 1.3 - - + -
147A TYR* 5.9 0.2 - - + -
148A CYS* 1.3 72.8 - - - +
150A CYS* 1.3 58.8 + - - +
178A ILE* 3.4 43.3 - - + +
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Residues in contact with CYS 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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35A LEU* 5.6 0.2 - - - +
64A SER* 4.0 1.8 - - - -
65A GLY* 4.7 2.0 - - - +
120A VAL* 3.9 12.8 - - + -
149A LEU* 1.3 75.7 - - - +
151A GLY* 1.3 58.7 + - - +
154A ASP* 3.5 22.0 - - + +
155A LEU* 3.9 28.3 - - - -
177A LEU* 3.8 22.7 - - + -
178A ILE 2.9 7.3 + - - +
179A TYR* 3.9 18.6 - - - -
180A ASP* 2.9 30.8 + - - +
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Residues in contact with GLY 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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65A GLY* 5.3 1.6 - - - +
150A CYS* 1.3 75.3 - - - +
152A ASP* 1.3 67.3 + - - -
153A GLY 3.2 2.5 - - - -
154A ASP* 3.0 20.4 + - - +
155A LEU* 3.3 15.6 + - - +
179A TYR* 3.7 6.7 - - - -
180A ASP* 4.0 13.2 - - - -
5001A TPP 3.6 12.3 - - - -
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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