Contacts of the strand formed by residues 145 - 150 (chain L) in PDB entry 1CZ8
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 LYS 145 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144L ALA* 1.3 75.8 - - - +
146L VAL* 1.3 67.7 + - - +
147L GLN* 3.7 34.3 + - - -
161L GLU* 5.3 0.7 - - - -
195L GLU* 3.5 7.9 + - - +
196L VAL* 3.4 6.2 - - - +
197L THR* 3.0 61.7 + - + +
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Residues in contact with VAL 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134L CYS* 4.4 5.6 - - - -
136L LEU* 4.0 18.8 - - + -
145L LYS* 1.3 82.5 - - - +
147L GLN* 1.3 62.0 + - - +
148L TRP* 4.2 10.7 + - - +
161L GLU* 3.6 23.7 + - - +
175L LEU* 3.7 25.8 - - + -
177L SER* 4.0 20.9 - - - +
194L CYS* 4.2 22.7 - - + -
195L GLU 3.5 4.5 - - - +
196L VAL* 4.8 1.8 - - + -
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Residues in contact with GLN 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L LYS* 3.7 28.4 + - - -
146L VAL* 1.3 75.8 - - - +
148L TRP* 1.3 65.7 + - - +
149L LYS* 3.7 28.9 - - - +
154L LEU* 3.3 30.5 - - + +
193L ALA 3.6 0.9 - - - +
194L CYS* 3.2 5.4 - - - -
195L GLU* 2.7 72.5 + - - +
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Residues in contact with TRP 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L ILE* 4.0 11.4 - - + -
132L VAL* 3.6 43.3 - - + -
133L VAL 3.9 1.3 - - - -
134L CYS* 3.5 27.6 - - + -
146L VAL* 4.2 8.6 - - + +
147L GLN* 1.3 75.1 - - - +
149L LYS* 1.3 68.9 + - - +
150L VAL* 6.0 0.2 - - + -
154L LEU* 3.4 6.1 - - - +
155L GLN* 2.8 50.2 + - + +
159L SER* 3.8 27.1 - - - -
177L SER* 3.0 42.5 + - - -
179L LEU* 3.8 20.6 - - + -
192L TYR* 5.5 1.8 - + + -
193L ALA 3.5 19.3 - - - -
194L CYS* 3.9 14.1 - - + -
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Residues in contact with LYS 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L GLN* 3.7 26.9 - - - +
148L TRP* 1.3 81.1 - - - +
150L VAL* 1.3 64.3 + - - +
151L ASP 4.0 0.2 - - - -
152L ASN* 3.0 51.8 + - - +
153L ALA 3.0 12.6 - - - +
154L LEU* 3.9 14.4 - - - -
191L VAL 3.5 3.5 - - - +
192L TYR* 3.8 0.9 - - - -
193L ALA* 3.0 42.9 + - + +
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Residues in contact with VAL 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L TRP* 6.0 0.2 - - + -
149L LYS* 1.3 73.8 - - - +
151L ASP* 1.3 70.6 + - - +
153L ALA* 2.8 27.0 + - + +
155L GLN* 3.7 31.4 - - + +
179L LEU* 4.0 13.0 - - + -
181L LEU* 4.5 6.3 - - + -
189L HIS* 3.6 41.0 - - + +
191L VAL 3.4 3.4 - - - +
192L TYR* 3.6 32.8 - - + +
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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