Contacts of the strand formed by residues 154 - 159 (chain A) in PDB entry 4LP4
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 THR 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLY* 1.3 79.6 - - - +
155A LEU* 1.3 69.7 + - - +
156A SER* 6.1 0.3 - - - -
175A GLU* 5.9 3.8 - - - +
188A LEU* 3.8 6.6 - - - +
209A SER 3.8 0.5 - - - +
210A PHE* 3.5 5.4 - - - -
211A SER* 2.9 46.7 + - - -
213A GLY* 5.9 0.9 - - - -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 4.9 0.9 - - + -
144A CYS* 3.5 33.4 - - + +
146A SER* 3.8 22.9 - - - +
154A THR* 1.3 82.7 - - - +
156A SER* 1.3 63.1 + - - +
173A VAL* 6.0 0.5 - - - +
175A GLU* 4.1 17.4 + - - +
188A LEU* 3.7 34.0 - - + +
189A GLN 3.9 0.7 - - - +
190A SER* 3.8 26.3 + - - -
208A CYS* 4.0 15.7 - - - -
209A SER 3.5 11.7 - - - +
210A PHE* 4.1 11.7 - - + -
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A THR* 5.5 0.6 + - - -
155A LEU* 1.3 77.0 - - - +
157A TRP* 1.3 71.3 + - - +
158A HIS* 3.9 8.8 + - - -
164A LEU 5.8 1.8 - - - -
208A CYS* 3.4 5.1 - - - -
209A SER* 3.0 43.4 + - - -
211A SER* 4.8 7.1 + - - -
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Residues in contact with TRP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.7 26.7 - - + -
141A VAL* 5.1 0.7 - - + -
142A GLY* 3.6 28.3 - - - -
143A THR 4.1 1.6 - - - -
144A CYS* 3.6 22.4 - - + +
156A SER* 1.3 81.1 - - - +
158A HIS* 1.3 68.9 + - - +
163A PRO* 3.8 1.0 - - - +
164A LEU* 2.9 38.6 + - + +
173A VAL* 4.2 11.4 - - + -
190A SER* 3.0 45.6 + - - -
192A LEU* 3.4 50.6 - - + +
206A PHE* 4.7 1.3 - - + -
207A SER 3.3 22.7 - - - -
208A CYS* 4.2 4.2 - - + -
225A ILE* 4.4 11.0 - - + -
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Residues in contact with HIS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A SER* 3.9 13.9 + - - -
157A TRP* 1.3 81.3 + - - +
159A LEU* 1.3 61.3 + - - +
160A ASP 4.2 0.2 - - - -
161A GLY 4.9 1.7 - - - +
162A LYS* 3.2 11.9 + - - +
163A PRO* 3.7 29.4 - - + +
164A LEU* 4.3 4.3 - - - +
205A THR 3.6 0.7 - - - +
206A PHE* 3.2 8.7 - - - +
207A SER* 2.7 55.1 + - - +
209A SER* 3.0 30.1 + - - -
221A ARG* 3.7 30.7 + - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A HIS* 1.3 72.5 - - - +
160A ASP* 1.3 79.2 + - + +
161A GLY 3.2 0.9 - - - -
162A LYS* 2.9 26.0 + - - +
164A LEU* 4.1 30.6 - - + +
204A PRO* 3.7 25.8 - - + -
205A THR 3.3 11.7 - - - +
206A PHE* 3.6 25.1 - - + -
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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