Contacts of the strand formed by residues 140 - 145 (chain A) in PDB entry 5JPM
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 HIS 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ARG* 5.8 1.3 - - - -
139A GLY* 1.3 77.2 - - - -
141A LEU* 1.3 62.8 + - - +
142A PHE* 3.7 21.5 - + + -
161A PHE 3.7 1.6 - - - +
162A ALA* 3.7 1.0 - - - -
163A LEU* 2.7 45.9 + - + +
164A ASP 2.9 24.7 + - - -
165A GLN* 3.6 23.3 - - - -
167A MET* 3.7 17.3 - - - -
219A PHE* 4.5 0.4 - - - -
627A ALA* 3.6 23.3 - - + -
628A MET* 3.6 23.5 + - + -
630A SER* 4.8 0.9 - - - -
631A TYR* 3.4 25.7 - + - -
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Residues in contact with LEU 141 (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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138A ARG 5.6 0.2 - - - +
139A GLY 4.4 0.2 - - - -
140A HIS* 1.3 72.6 - - - +
142A PHE* 1.3 66.3 + - - +
143A LEU* 4.4 1.3 - - + -
160A VAL* 4.4 14.4 - - + -
161A PHE 3.3 14.1 - - - +
162A ALA* 3.8 19.1 - - + -
174A ILE* 4.3 9.0 - - + -
217A ALA 3.4 25.6 - - - +
218A ARG* 3.6 17.5 - - - -
219A PHE* 3.8 31.0 - - + +
225A SER* 3.8 12.6 - - - +
227A SER* 2.8 40.0 + - - +
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Residues in contact with PHE 142 (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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140A HIS* 3.7 27.1 - + + -
141A LEU* 1.3 78.4 - - - +
143A LEU* 1.3 59.7 + - - +
160A VAL* 3.2 2.0 - - - +
161A PHE* 2.5 58.9 + - + -
163A LEU* 3.8 25.4 - - + -
167A MET* 4.3 10.1 - - + -
619A LEU* 4.1 31.6 - - + -
623A LYS 4.5 1.8 - - - -
624A VAL* 4.2 24.7 - - + -
627A ALA* 3.6 33.0 - - + -
811B LEU* 6.2 0.2 - - + -
819B LEU* 4.1 11.0 - - + -
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Residues in contact with LEU 143 (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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141A LEU 4.0 4.7 - - - +
142A PHE* 1.3 77.0 - - - +
144A GLN* 1.3 64.2 + - - +
158A TYR* 5.8 3.6 - - + -
159A ARG 3.2 11.2 - - - +
160A VAL* 3.9 15.0 - - + -
176A VAL* 5.8 0.4 - - + -
215A ILE* 3.3 42.8 - - + +
217A ALA* 4.2 11.2 - - + +
227A SER* 3.4 42.0 - - - +
228A SER* 3.9 3.6 - - - +
229A THR* 3.4 30.7 + - + +
619A LEU* 5.4 5.9 - - - +
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Residues in contact with GLN 144 (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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143A LEU* 1.3 77.8 - - - +
145A THR* 1.3 69.2 + - - +
158A TYR* 3.3 2.9 - - - +
159A ARG* 2.8 77.8 + - + +
161A PHE* 4.0 4.9 - - + -
229A THR* 4.2 5.8 - - - +
618A PRO* 5.7 3.8 - - - +
619A LEU* 4.3 23.7 - - + +
784B TRP* 4.7 2.4 - - - +
811B LEU* 3.6 26.0 - - - +
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Residues in contact with THR 145 (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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144A GLN* 1.3 82.7 - - - +
146A ASP* 1.3 66.1 + - - +
147A GLN* 2.6 22.9 + - - +
148A PRO* 4.5 1.4 - - - +
150A TYR* 3.5 12.7 - - - -
156A VAL* 4.3 4.9 - - + -
157A ARG 3.3 6.5 - - - +
158A TYR* 3.9 16.4 - - + -
215A ILE* 3.9 17.9 - - + -
229A THR* 4.6 12.1 + - + +
230A GLN 6.2 0.4 - - - -
231A PHE* 4.2 20.9 - - + +
604A LEU* 5.5 1.7 - - - +
784B TRP* 4.5 3.4 + - - -
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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