Contacts of the strand formed by residues 166 - 174 (chain B) in PDB entry 4ZPK
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 ARG 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLU* 5.0 5.2 + - - -
146B ASN* 3.0 50.7 + - - +
148B THR 3.1 24.0 + - - -
149B LEU* 3.7 18.6 + - - +
163B SER 3.9 11.5 + - - -
164B THR* 3.7 12.7 + - - +
165B GLU* 1.3 102.9 + - - +
167B ASP* 1.3 63.6 + - - +
168B PHE* 4.4 7.9 - - + -
195B CYS 4.4 1.8 - - - -
196B THR* 3.4 2.6 - - - -
197B GLY 2.9 38.8 + - - +
199B VAL* 3.8 22.9 - - + +
222B LEU* 3.9 13.2 - - + -
224B ILE* 4.8 0.4 - - + -
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Residues in contact with ASP 167 (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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344A GLN* 4.5 22.4 + - - +
345A VAL 4.8 6.0 - - - +
146B ASN* 4.6 2.5 + - - +
166B ARG* 1.3 76.8 - - - +
168B PHE* 1.3 66.3 + - - +
169B PHE* 5.0 1.7 - - - -
194B HIS* 3.0 26.2 + - - -
195B CYS 3.3 4.5 - - - -
196B THR* 3.4 20.0 - - - +
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Residues in contact with PHE 168 (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 GLU* 4.0 10.5 - - + +
143B ILE* 4.4 9.4 - - + -
146B ASN* 3.2 53.4 - - + +
166B ARG* 4.4 10.3 - - + -
167B ASP* 1.3 82.8 + - - +
169B PHE* 1.3 97.1 + - - +
170B MET* 4.2 18.4 - - + -
194B HIS* 3.6 3.6 + - - -
195B CYS* 2.8 62.6 + - + +
222B LEU* 4.7 8.1 - - + -
224B ILE* 4.3 16.2 - - + -
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Residues in contact with PHE 169 (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 ASP* 5.1 0.7 - - - +
142B GLU* 3.1 21.7 + - - +
143B ILE* 5.4 0.2 - - - +
167B ASP* 5.0 1.3 - - - -
168B PHE* 1.3 87.1 - - - +
170B MET* 1.3 63.1 + - - +
192B VAL* 4.7 6.3 - - + -
193B LEU 3.1 17.5 - - - +
194B HIS* 3.2 44.2 - + + -
195B CYS 4.7 0.2 - - - +
229B ILE* 4.4 6.5 - - + -
291B LYS* 4.2 11.9 - - - -
295B ASN* 3.8 16.6 - - + +
299B LYS* 3.5 28.0 + - + -
301B GLN 4.6 9.9 - - - -
302B VAL* 4.1 13.0 - - + -
303B VAL* 3.4 42.4 - - + -
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Residues in contact with MET 170 (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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131B ILE* 4.3 12.1 - - + -
135B THR* 3.8 18.6 - - + -
139B ASP* 3.6 7.0 - - - -
143B ILE* 3.5 50.9 - - + -
168B PHE* 4.2 9.0 - - + -
169B PHE* 1.3 75.7 - - - +
171B ARG* 1.3 64.2 + - - +
172B MET* 4.9 2.0 - - + +
192B VAL* 3.7 2.8 - - - -
193B LEU* 2.9 47.5 + - + +
195B CYS* 3.3 28.0 - - - -
224B ILE* 4.7 8.1 - - + -
226B CYS* 5.2 2.7 - - - -
299B LYS* 4.7 0.4 - - - -
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Residues in contact with ARG 171 (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 THR* 3.3 7.3 - - - -
136B HIS* 2.8 77.5 + - + -
138B CYS* 3.7 11.7 - - - +
139B ASP* 2.7 37.2 + - - +
170B MET* 1.3 73.4 - - - +
172B MET* 1.3 60.8 + - - +
190B TRP* 4.2 16.1 - - + -
191B LYS 3.8 4.0 - - - +
192B VAL* 4.5 18.8 - - + -
298B THR* 3.5 26.1 + - - -
299B LYS* 4.2 20.6 - - + +
300B GLY 4.8 3.1 - - - +
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Residues in contact with MET 172 (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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98B PHE* 3.9 17.7 - - + -
108B MET* 4.4 18.6 - - - -
111B LEU* 4.9 1.8 - - + -
115B ILE* 4.8 6.1 - - + -
119B MET* 4.0 13.5 - - + +
121B LEU* 5.9 1.6 - - + -
126B LEU* 4.3 24.0 - - + -
131B ILE* 4.7 6.1 - - + -
134B PHE* 3.7 20.6 - - + +
135B THR* 4.5 11.2 - - + -
170B MET* 3.8 3.5 + - + +
171B ARG* 1.3 74.8 - - - +
173B LYS* 1.3 68.1 + - - +
190B TRP* 3.6 8.2 - - - -
191B LYS* 2.9 34.2 + - - +
193B LEU* 3.6 33.2 - - + -
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Residues in contact with LYS 173 (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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119B MET* 4.0 19.2 - - - +
121B LEU* 4.3 20.4 - - + +
133B ASP 4.1 17.1 + - - +
134B PHE* 3.1 26.6 + - + +
172B MET* 1.3 80.7 - - + +
174B CYS* 1.3 61.2 + - - +
175B THR* 6.0 1.1 - - + -
185B LEU* 4.1 22.6 - - + +
188B ALA* 3.8 26.0 - - + +
189B THR 3.8 4.0 - - - -
190B TRP* 3.5 31.9 - - + -
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Residues in contact with CYS 174 (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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118B PHE 3.4 24.7 - - - -
119B MET* 3.4 9.0 - - - +
121B LEU* 5.4 0.2 - - - -
173B LYS* 1.3 77.4 - - - +
175B THR* 1.3 70.3 + - - +
176B VAL* 3.7 18.2 - - - -
177B THR 4.4 3.6 - - - -
187B SER 3.8 0.7 - - - +
188B ALA* 3.7 0.9 - - - -
189B THR* 2.9 48.8 + - - +
191B LYS* 3.7 32.3 - - + -
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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