Contacts of the strand formed by residues 154 - 160 (chain B) in PDB entry 2Z9I
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 VAL 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B THR 4.2 6.7 + - - +
87B SER* 6.0 0.5 - - - -
141B PRO* 4.8 0.9 - - + -
142B VAL 3.1 11.9 - - - +
143B SER* 4.3 8.5 - - - -
152B ASN* 4.4 8.3 - - + +
153B THR* 1.3 79.4 - - - +
155B LEU* 1.3 65.1 + - - +
156B ASP 4.1 0.5 + - - -
278B ASP* 3.8 22.7 - - + +
281B VAL* 4.1 19.3 - - + -
282B ALA* 3.6 38.1 - - + +
285B ARG* 4.7 22.9 + - - +
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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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87B SER 4.6 7.0 - - - +
88B ASP* 4.8 6.5 - - + +
140B ARG 3.3 0.3 - - - +
141B PRO* 3.3 6.6 - - - +
142B VAL* 2.7 61.4 + - + +
144B THR 4.9 4.7 - - - +
153B THR* 4.7 11.9 - - - +
154B VAL* 1.3 74.7 - - - +
156B ASP* 1.3 58.7 + - - +
157B ALA* 3.5 9.0 - - + +
185B SER* 4.3 12.8 - - - -
186B ALA* 4.1 19.7 - - + -
206B PHE* 4.2 13.9 - - + +
207B ALA 5.4 0.2 - - - -
208B ILE* 3.8 33.4 - - + -
282B ALA* 3.6 4.6 - - - +
410E GLN* 5.0 4.5 - - - +
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Residues in contact with ASP 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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139B ASN* 3.1 45.1 + - - +
140B ARG 3.8 2.0 - - - -
154B VAL 4.1 0.6 + - - -
155B LEU* 1.3 71.6 - - - +
157B ALA* 1.3 58.0 + - - +
208B ILE* 6.2 0.2 - - - +
209B PRO* 3.2 26.5 - - - +
212B GLN* 3.2 28.7 + - - +
282B ALA* 3.4 29.4 + - - +
283B ALA* 4.7 3.6 + - - +
286B SER* 3.5 20.5 + - - -
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Residues in contact with ALA 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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138B LEU 3.7 0.3 - - - -
139B ASN 3.1 9.1 + - - -
140B ARG* 2.7 45.7 + - + +
142B VAL* 3.9 7.0 - - + -
155B LEU* 4.3 9.6 - - + -
156B ASP* 1.3 73.8 - - - +
158B ILE* 1.3 61.8 + - - +
159B GLN 3.7 0.9 + - - -
206B PHE* 3.7 38.4 - - + -
207B ALA 3.5 9.0 - - - +
209B PRO* 5.0 0.2 - - - -
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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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108B SER* 5.1 0.7 - - - -
111B LEU* 3.7 30.3 - - + -
135B VAL* 4.3 13.0 - - + -
137B ALA 3.8 4.5 - - - -
138B LEU* 4.0 9.0 - - + -
156B ASP 3.9 0.8 + - - -
157B ALA* 1.3 71.7 - - - +
159B GLN* 1.3 72.4 + - - +
160B THR* 5.2 0.3 - - - +
173B LEU* 3.9 22.2 - - + -
181B VAL 3.4 26.5 - - - +
182B GLY* 4.3 6.5 - - - -
205B GLY 3.7 0.2 - - - +
206B PHE* 3.2 6.2 - - - -
207B ALA* 2.8 39.0 + - + +
209B PRO* 3.6 30.3 - - + -
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Residues in contact with GLN 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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135B VAL* 3.5 6.1 - - - -
136B SER* 2.7 33.5 + - - -
137B ALA* 3.0 21.8 + - + +
140B ARG* 2.8 43.3 - - + +
157B ALA 3.7 1.6 + - - -
158B ILE* 1.3 75.7 - - - +
160B THR* 1.3 59.5 + - - +
203B GLY 5.6 0.2 - - - +
204B LEU* 3.6 12.8 - - - +
205B GLY 3.2 17.3 - - - +
206B PHE* 3.6 22.8 - - + -
126C LEU* 4.0 8.6 - - - +
129C THR* 3.0 32.3 + - - +
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Residues in contact with THR 160 (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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117B VAL* 3.5 13.2 - - - +
134B ILE 2.9 18.1 + - - -
135B VAL* 4.8 0.7 - - - -
136B SER* 3.8 5.4 - - - -
158B ILE 5.2 1.8 - - - +
159B GLN* 1.3 75.1 - - - +
161B ASP* 1.3 62.8 + - - +
162B ALA* 3.1 20.4 + - + +
164B ILE* 3.5 30.7 - - + -
173B LEU* 4.1 22.0 - - + -
184B ASN* 4.5 0.7 - - - +
203B GLY 3.4 3.2 - - - +
204B LEU* 4.1 0.3 - - - -
205B GLY* 2.9 36.6 + - - +
206B PHE* 5.4 0.7 - - - -
207B ALA 5.5 0.7 - - - +
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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