Contacts of the strand formed by residues 154 - 159 (chain B) in PDB entry 4ZCH
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 CYS 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B VAL* 4.0 16.6 - - - -
108B VAL* 4.1 15.7 - - + -
142B LEU* 4.8 2.7 - - + -
152B GLN 4.6 1.3 - - - -
153B ASP* 1.3 76.1 - - - +
155B LEU* 1.3 63.9 + - - +
180B PHE* 3.8 30.5 - - - -
181B LYS* 3.4 2.8 - - - +
182B ARG* 3.1 46.8 + - - +
186B LEU* 4.1 7.0 - - - +
289B ALA 3.4 11.7 - - - +
290B LEU* 4.3 8.5 - - + -
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 6.6 0.2 - - - -
154B CYS* 1.3 75.9 - - - +
156B GLN* 1.4 61.1 + - - +
157B LEU* 3.6 36.3 - - + -
178B LEU* 3.7 13.2 - - + -
180B PHE* 3.3 5.6 - - - +
181B LYS* 3.7 13.2 - - + -
186B LEU* 3.4 38.6 - - + +
187B GLU* 3.5 22.7 - - - +
188B GLU* 3.8 5.6 - - + +
193B ILE* 4.2 18.2 - - + -
204B TYR* 4.3 1.8 + - - -
288B GLY* 3.2 3.6 - - - -
289B ALA 3.0 32.3 + - - +
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Residues in contact with GLN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU 5.6 0.2 + - - -
107B GLY* 3.7 6.8 - - - -
108B VAL* 3.0 32.1 + - + +
109B PHE* 3.7 21.8 - - - -
155B LEU* 1.4 73.5 - - - +
157B LEU* 1.3 64.8 - - - +
158B ILE* 4.1 18.6 - - - +
178B LEU* 3.9 2.6 - - - +
179B SER* 2.8 39.8 + - - -
180B PHE* 2.8 24.5 + - + +
204B TYR* 2.9 31.8 + - + +
286B PHE* 4.6 11.3 - - + +
287B PHE 3.7 8.1 - - - +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 3.6 20.6 - - + -
156B GLN* 1.3 73.4 - - - +
158B ILE* 1.3 62.5 + - - +
176B TRP* 3.9 37.0 - - + -
177B LEU 3.3 15.0 - - - +
178B LEU* 3.9 10.3 - - + -
188B GLU* 3.5 31.4 - - + -
191B ASN 5.0 0.4 - - - +
192B LYS 4.7 5.2 - - - -
193B ILE* 3.6 24.9 - - + -
286B PHE* 3.2 6.8 - - - +
287B PHE* 2.7 50.3 + - + +
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Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ASN* 3.5 41.5 - - + +
156B GLN* 4.1 10.8 - - - +
157B LEU* 1.3 79.8 - - - +
159B ALA* 1.3 72.0 + - - +
176B TRP* 3.5 7.8 - - - -
177B LEU* 2.8 47.4 + - + +
179B SER* 3.8 28.5 - - - +
282B GLY* 3.5 30.3 - - - +
285B THR 3.9 2.9 - - - -
286B PHE* 4.0 5.6 - - + -
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ILE* 1.3 78.1 - - - +
160B ASP* 1.3 59.0 + - - +
161B SER 3.8 2.6 + - - -
174B VAL* 4.0 7.2 - - + -
175B PRO 3.7 6.1 - - - -
176B TRP* 3.6 5.2 - - - -
177B LEU* 3.9 9.0 - - - +
280B LEU* 3.7 31.5 - - + +
281B ASP 4.0 2.0 - - - +
282B GLY* 4.0 9.1 + - - -
285B THR* 3.0 39.7 + - + +
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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