Contacts of the strand formed by residues 154 - 162 (chain B) in PDB entry 2ZUQ
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 GLY 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B GLN* 3.0 26.9 + - - +
150B LEU* 3.1 16.5 + - - +
152B SER 3.9 0.4 + - - -
153B GLY* 1.3 77.8 - - - +
155B ALA* 1.3 61.8 + - - +
206B LEU 4.8 2.2 - - - -
207B THR* 4.4 1.3 - - - -
208B LYS* 3.5 14.3 - - - +
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Residues in contact with ALA 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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145B PRO* 4.1 4.3 - - + -
149B GLN* 3.8 6.3 + - - +
150B LEU* 3.5 21.1 - - + -
154B GLY* 1.3 76.1 - - - +
156B SER* 1.3 64.1 + - - +
157B VAL* 5.2 1.4 - - - +
206B LEU* 2.9 35.4 + - - +
207B THR 3.7 8.1 - - - +
208B LYS* 4.1 2.1 - - - +
211B TYR* 3.7 29.8 - - + -
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PHE 4.3 0.3 - - - +
144B PRO 4.0 1.0 - - - +
145B PRO* 3.4 23.7 - - - +
149B GLN* 2.5 32.4 + - - +
155B ALA* 1.3 74.8 + - - +
157B VAL* 1.3 63.9 + - - +
158B VAL* 4.3 2.9 + - - +
203B THR* 4.5 7.0 - - - -
204B LEU 3.4 8.5 - - - -
205B THR* 3.7 18.1 + - - -
206B LEU 5.3 0.2 + - - -
130C LEU* 5.9 1.9 - - - +
147C LEU* 4.4 17.3 - - - +
149C LYS* 4.4 11.1 + - - +
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Residues in contact with VAL 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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142B ILE* 3.9 14.6 - - + -
143B PHE 3.4 15.5 - - - +
144B PRO* 4.3 0.2 - - + -
145B PRO* 3.2 25.8 - - + -
155B ALA 5.2 0.9 - - - +
156B SER* 1.3 74.3 - - - +
158B VAL* 1.3 60.0 + - - +
173B TRP* 3.1 28.3 - - + -
204B LEU* 2.7 48.7 + - + +
206B LEU* 5.9 3.6 - - + -
211B TYR* 4.0 17.7 - - + -
217B TYR* 5.3 9.0 - - + -
234B PHE* 3.9 13.7 - - + -
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ILE* 3.6 0.7 - - - +
143B PHE* 2.7 52.0 + - + +
156B SER 5.1 2.0 - - - +
157B VAL* 1.3 77.9 - - - +
159B CYS* 1.3 58.5 + - - +
160B PHE* 4.3 15.0 - - + -
173B TRP* 3.8 3.6 - - - -
201B SER* 6.0 1.3 - - - -
202B SER 3.3 8.3 - - - +
203B THR* 3.1 34.1 - - + +
130C LEU* 3.7 31.0 - - + -
147C LEU* 3.7 20.2 - - + -
184C SER* 5.5 1.1 - - - -
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Residues in contact with CYS 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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140B VAL* 3.7 7.2 - - + -
141B SER 3.3 15.0 - - - +
142B ILE* 3.7 10.3 - - - -
143B PHE* 4.8 0.2 - - - -
158B VAL* 1.3 75.1 - - - +
160B PHE* 1.3 65.1 + - - +
161B LEU* 3.5 7.7 - - - +
171B VAL* 5.4 1.3 - - - -
173B TRP* 3.3 22.4 - - - -
201B SER* 3.7 0.8 - - - -
202B SER* 3.2 27.5 + - - -
219B CYS* 2.0 51.6 - - - -
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Residues in contact with PHE 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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139B THR 3.7 1.7 - - - +
140B VAL* 3.1 25.8 - - - +
141B SER* 3.3 15.0 + - - +
143B PHE* 3.6 34.3 - + - -
158B VAL* 4.3 8.5 - - + -
159B CYS* 1.3 74.7 - - - +
161B LEU* 1.3 59.8 + - - +
162B ASN* 3.3 17.9 - - - +
200B MET 3.7 2.5 - - - +
201B SER* 3.6 8.3 - - - -
130C LEU* 3.9 19.7 - - + -
143C THR* 4.8 1.6 - - - +
144C LEU 4.6 0.2 - - - -
145C GLY* 4.1 11.0 - - - -
172C PHE* 3.3 34.3 - + - -
184C SER* 3.7 17.0 - - - -
185C SER 3.7 18.6 - - - -
186C SER* 3.5 20.4 - - - -
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Residues in contact with LEU 161 (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 PRO* 4.4 6.1 - - + -
139B THR 4.4 4.0 - - - +
140B VAL* 3.6 27.8 - - + -
159B CYS* 3.5 20.4 - - + +
160B PHE* 1.3 71.9 - - - +
162B ASN* 1.3 64.0 + - - +
164B PHE* 3.0 37.8 - - + -
169B ILE* 3.7 18.6 - - + -
171B VAL* 3.7 35.7 - - + -
199B SER* 3.5 0.5 - - - -
200B MET* 3.0 34.4 + - + +
202B SER* 4.8 0.4 - - - +
220B GLU 5.6 0.2 - - - -
221B ALA* 4.1 12.3 - - + +
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Residues in contact with ASN 162 (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 PRO* 3.7 0.5 - - - +
139B THR* 3.0 41.0 + - - +
141B SER* 5.7 0.9 - - - -
160B PHE* 3.3 24.0 - - - +
161B LEU* 1.3 75.6 + - - +
163B ASN* 1.3 78.8 + - - +
164B PHE 3.2 1.7 + - - -
199B SER* 4.4 4.3 - - - -
143C THR* 4.9 8.7 + - - +
170C HIS* 3.4 17.4 + - + -
172C PHE* 4.2 5.2 - - - -
186C SER* 2.9 25.9 + - - -
188C THR* 3.7 21.1 + - - +
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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