Contacts of the strand formed by residues 153 - 159 (chain F) in PDB entry 4PJ7
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 153 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121F PRO* 4.5 2.2 - - + -
145F ALA* 5.8 0.4 - - + -
148F PHE* 3.6 48.7 - - + -
151F ASP 3.1 8.1 + - - +
152F HIS* 1.3 78.9 - - - +
154F GLU* 1.3 67.4 + - - +
155F LEU 4.2 0.2 - - - -
174F PRO* 5.7 2.5 - - + -
188F LEU* 4.1 22.1 - - + +
210F VAL* 3.9 17.5 - - + -
211F GLN 3.2 11.4 - - - +
212F PHE* 3.9 14.4 - - + -
213F TYR* 5.1 0.4 - - - -
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Residues in contact with GLU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F THR* 5.7 0.7 + - - -
10F SER* 5.3 1.0 + - - -
153F VAL* 1.3 78.3 - - - +
155F LEU* 1.3 62.1 + - - +
156F SER* 5.2 1.3 + - - -
209F GLN* 3.6 1.6 + - - +
210F VAL* 3.4 4.2 - - - -
211F GLN* 2.9 43.7 + - + +
213F TYR* 3.1 39.4 + - + -
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Residues in contact with LEU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F CYS* 4.4 4.9 - - - -
145F ALA* 4.8 2.9 - - + -
153F VAL 4.2 0.4 - - - -
154F GLU* 1.3 73.1 - - - +
156F SER* 1.3 68.9 + - - +
157F TRP* 4.1 7.6 - - + +
170F THR* 4.1 16.2 + - + +
188F LEU* 4.0 38.3 - - + +
189F SER 4.6 0.9 - - - -
190F SER* 3.5 40.4 - - - +
208F CYS* 3.7 22.2 - - - -
209F GLN 3.3 3.6 - - - -
210F VAL* 3.9 23.8 - - + +
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Residues in contact with SER 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F GLU 5.2 1.1 + - - -
155F LEU* 1.3 79.4 - - - +
157F TRP* 1.3 62.1 + - - +
158F TRP* 2.7 28.3 + - - -
163F GLU* 3.5 25.4 - - - -
168F VAL* 6.4 0.4 - - - -
208F CYS* 3.6 2.1 - - - -
209F GLN* 2.7 52.1 + - - +
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Residues in contact with TRP 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F VAL* 4.5 7.2 - - + -
141F LEU* 3.8 33.9 - - + -
142F VAL 4.2 2.7 - - - -
143F CYS* 3.5 39.3 - - + -
155F LEU* 4.1 6.9 - - + +
156F SER* 1.3 70.1 - - - +
158F TRP* 1.3 63.3 + - - +
163F GLU* 3.3 8.8 - - - +
164F VAL* 3.0 47.1 + - + +
168F VAL* 3.6 25.5 - - + +
190F SER* 2.8 34.4 + - - -
191F ARG 4.0 4.4 + - - -
192F LEU* 3.6 32.1 - - + -
206F PHE* 4.8 4.0 - - + -
207F ARG* 3.5 22.0 - - - -
208F CYS* 4.0 15.9 - - + -
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Residues in contact with TRP 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F SER* 2.7 32.3 + - - -
157F TRP* 1.3 77.1 - - - +
159F VAL* 1.3 62.5 - - - +
160F ASN 4.0 0.7 + - - -
161F GLY* 3.6 25.9 + - - +
162F LYS* 3.4 7.6 - - - +
163F GLU* 3.3 51.1 - - + -
205F HIS* 3.8 1.9 - - - +
206F PHE* 3.5 1.7 - - - -
207F ARG* 2.8 67.0 + - + +
209F GLN* 3.7 31.7 - - + -
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Residues in contact with VAL 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F TRP* 4.2 0.4 - - + -
158F TRP* 1.3 73.4 - - - +
160F ASN* 1.3 72.6 - - - +
161F GLY 3.2 0.9 - - - -
162F LYS* 2.8 32.1 + - - +
164F VAL* 3.8 33.2 - - + +
192F LEU* 3.9 12.3 - - + -
194F VAL* 5.6 2.0 - - + -
198F PHE* 3.6 36.3 - - + -
204F ASN* 4.8 0.2 - - - +
205F HIS 3.3 8.1 - - - +
206F PHE* 3.7 24.2 - - + -
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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