Contacts of the strand formed by residues 150 - 154 (chain A) in PDB entry 4CBS
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 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA 6.0 0.2 - - - -
90A LEU* 3.7 20.6 - - + -
93A VAL* 3.8 20.4 - - + -
94A LEU* 3.9 16.6 - - + -
99A SER 3.6 0.6 + - - -
100A PHE* 3.4 29.9 - - + -
101A LEU 2.9 24.8 + - - -
148A PRO* 3.4 4.9 - - - +
149A VAL* 1.3 83.1 - - - +
151A LEU* 1.3 59.2 + - - +
178A CYS* 3.5 5.4 - - - -
179A LEU* 3.5 22.7 - - + +
181A LEU* 3.5 27.4 - - + +
202A ILE* 3.7 19.5 - - + -
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Residues in contact with LEU 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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101A LEU* 3.1 52.5 - - + +
126A MET* 3.8 15.9 - - + -
139A VAL* 3.7 24.9 - - + -
143A LEU* 4.7 1.8 - - + -
150A LEU* 1.3 78.4 - - - +
152A PHE* 1.3 64.7 + - - +
153A LEU* 3.7 28.3 - - + -
169A PHE* 5.2 0.9 - - + -
173A CYS* 3.8 14.1 - - - -
178A CYS* 3.5 4.4 - - - -
179A LEU 2.8 14.6 + - - +
180A LEU* 3.8 11.0 - - + +
181A LEU* 2.6 35.3 + - - +
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Residues in contact with PHE 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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86A LEU* 4.0 10.8 - - + -
100A PHE* 3.8 23.7 - - + -
101A LEU 2.9 11.3 + - - +
102A VAL* 4.1 11.2 - - + -
103A GLY 3.1 27.1 + - - -
108A TRP* 4.0 14.4 - - + -
109A GLY* 3.5 18.6 - - - -
112A ALA* 3.9 9.9 - - + -
151A LEU* 1.3 74.4 - - - +
153A LEU* 1.3 69.5 + - - +
154A THR* 3.2 32.8 - - - -
181A LEU* 3.2 29.6 - - + -
183A ASP* 3.7 18.8 - - + -
204A TYR* 3.4 22.9 - + - -
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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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103A GLY* 4.5 6.7 - - - +
126A MET* 5.1 2.2 - - + -
134A TYR* 3.9 34.8 - - + -
139A VAL* 5.1 0.7 - - + -
151A LEU* 3.7 28.0 + - + -
152A PHE* 1.3 86.5 - - - +
154A THR* 1.3 59.9 - - - +
155A HIS 3.5 0.3 + - - -
164A GLN* 4.5 10.1 - - + +
166A LEU* 4.8 13.2 - - + -
169A PHE* 3.9 28.9 - - + -
180A LEU* 3.9 9.6 - - + -
181A LEU 2.6 12.3 + - - +
182A VAL* 3.1 13.4 - - + -
183A ASP* 2.8 30.8 + - - +
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Residues in contact with THR 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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103A GLY 5.0 2.2 + - - -
105A ASN* 4.2 15.8 + - - +
108A TRP* 3.6 20.0 - - + +
109A GLY 4.1 2.8 + - - -
152A PHE* 3.2 23.4 - - - -
153A LEU* 1.3 72.2 - - - +
155A HIS* 1.3 69.3 + - - +
156A GLY 3.5 24.5 - - - +
157A GLU* 3.6 27.1 + - + +
164A GLN* 3.2 17.3 - - - +
183A ASP* 3.9 9.4 - - + -
1389A PLP 4.2 6.3 - - + -
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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