Contacts of the strand formed by residues 178 - 187 (chain B) in PDB entry 4ZXB
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 TYR 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B GLU* 4.0 15.9 + - - +
111B ILE 5.0 0.5 + - - -
143B ASN* 3.2 6.3 + - - -
144B PHE* 2.8 56.2 + - + +
145B TYR* 3.9 22.2 - + - -
146B PRO 4.2 0.7 - - - -
147B LYS* 3.6 60.8 - - + +
168B TRP* 4.9 1.1 - - + -
169B THR* 3.9 15.7 - - - +
170B ASP* 4.9 0.7 - - - -
171B GLN* 3.5 50.2 + - + +
177B THR* 1.3 75.2 - - - +
179B SER* 1.3 65.4 + - - +
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Residues in contact with SER 179 (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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169A HIS* 2.9 32.8 + - - -
171A PHE* 3.7 7.6 - - - -
141B LEU 3.3 7.0 - - - -
142B ASN* 3.5 17.0 - - - -
143B ASN* 3.1 16.8 + - - -
144B PHE* 3.7 3.4 - - - -
168B TRP* 3.5 6.2 - - - -
169B THR* 3.0 36.8 + - - -
178B TYR* 1.3 74.5 + - - +
180B MET* 1.3 63.8 + - - +
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Residues in contact with MET 180 (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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171A PHE* 3.3 9.3 - - - -
139B CYS 4.0 0.2 - - - +
140B PHE* 3.7 1.7 - - - -
141B LEU* 2.8 52.9 + - + +
144B PHE* 4.2 7.0 - - + -
149B ILE* 4.1 13.7 - - + -
151B VAL* 3.7 15.9 - - + -
166B ASN* 3.4 41.3 - - + +
167B SER 3.1 17.9 - - - +
168B TRP* 3.6 37.0 - - + +
179B SER* 1.3 78.2 - - - +
181B SER* 1.3 63.0 + - - +
182B SER* 4.4 1.3 - - - -
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Residues in contact with SER 181 (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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171A PHE* 3.5 10.7 - - - +
183A SER* 3.3 26.4 + - - -
138B VAL* 5.0 0.7 - - - -
139B CYS 3.4 4.7 - - - -
140B PHE* 3.8 16.8 - - - -
141B LEU* 5.3 0.2 - - - -
165B LEU 4.8 1.0 + - - -
166B ASN* 3.2 4.0 - - - -
167B SER* 2.9 40.2 + - - -
180B MET* 1.3 79.0 - - - +
182B SER* 1.3 61.2 + - - +
183B THR* 4.0 10.2 + - - -
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 3.7 0.3 - - - -
139B CYS* 2.8 39.9 + - - -
141B LEU* 4.7 2.5 - - - -
151B VAL* 3.8 20.9 - - - +
153B TRP* 2.7 36.1 + - - -
164B VAL* 3.5 4.5 - - - +
165B LEU 3.4 0.2 - - - -
166B ASN* 2.8 23.6 + - - -
180B MET* 4.4 2.2 - - - -
181B SER* 1.3 73.8 - - - +
183B THR* 1.3 60.7 + - - +
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Residues in contact with THR 183 (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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146A LEU* 4.8 9.8 - - + +
148A LYS* 6.4 0.2 - - + -
181A THR* 5.7 5.2 - - + +
183A SER* 4.6 4.0 + - - -
136B SER* 4.0 17.0 - - - +
137B VAL 3.4 9.0 - - - +
138B VAL* 4.0 18.5 - - + +
153B TRP* 4.7 0.7 - - - -
163B GLY 3.6 2.1 - - - +
164B VAL* 3.4 4.7 - - - -
165B LEU* 2.8 48.2 + - + +
181B SER* 4.0 12.0 + - - -
182B SER* 1.3 76.6 + - - +
184B LEU* 1.3 61.1 + - - +
185B THR* 3.8 18.9 + - - +
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Residues in contact with LEU 184 (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 ALA 3.8 1.6 - - - +
136B SER* 3.5 0.9 - - - -
137B VAL* 2.8 45.1 + - + +
153B TRP* 3.9 39.4 - - + +
155B ILE* 3.8 28.3 - - + -
160B ARG* 4.0 11.4 - - + -
162B ASN 3.8 17.0 - - - +
163B GLY 3.6 12.8 - - - +
164B VAL* 3.8 13.0 - - + +
183B THR* 1.3 71.3 - - - +
185B THR* 1.3 59.9 + - - +
186B LEU* 4.1 23.3 - - + +
197B TYR* 4.6 5.6 - - + -
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Residues in contact with THR 185 (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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148A LYS* 4.0 19.8 - - - +
176A GLN* 5.9 2.5 - - - -
134B GLY* 6.2 0.2 - - - -
135B ALA 3.6 6.3 - - - +
136B SER* 3.3 23.9 + - - +
160B ARG* 4.9 1.4 + - - -
163B GLY* 3.2 21.3 + - - +
165B LEU* 5.6 6.1 - - - +
183B THR* 3.8 12.8 + - - +
184B LEU* 1.3 73.9 - - - +
186B LEU* 1.3 77.6 + - - +
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Residues in contact with LEU 186 (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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134B GLY* 4.4 1.4 - - - -
135B ALA 2.8 31.4 + - - +
137B VAL* 4.8 4.7 - - + -
155B ILE* 4.6 3.4 - - + -
160B ARG* 3.5 40.2 - - - +
184B LEU* 4.1 19.7 - - + +
185B THR* 1.3 87.7 - - - +
187B THR* 1.3 69.7 + - - +
190B GLU* 4.1 16.2 - - + +
191B TYR* 4.1 15.5 - - + +
194B HIS* 5.3 0.9 - - + -
197B TYR* 3.8 35.9 - - + +
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Residues in contact with THR 187 (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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133B GLY 4.3 6.1 - - - -
134B GLY* 5.1 0.4 - - - -
135B ALA* 4.2 0.9 - - - -
186B LEU* 1.3 77.1 - - - +
188B LYS* 1.3 59.7 + - - +
189B ASP* 3.8 7.1 + - - +
190B GLU* 2.9 29.3 + - + +
191B TYR* 2.8 27.2 + - - +
193B ARG* 4.8 1.6 + - - -
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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