Contacts of the strand formed by residues 140 - 145 (chain A) in PDB entry 5UQ9
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 SER 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLY 3.1 11.3 - - - +
128A VAL* 3.4 2.6 - - - -
129A SER* 3.0 40.6 + - - -
139A PRO* 1.3 70.9 - - - +
141A LEU* 1.3 62.1 + - - +
142A MET* 4.5 7.9 - - - +
170A CYS 3.9 5.6 - - - -
361A MET* 3.2 18.2 + - - -
364A GLY 2.6 26.2 + - - -
365A GLY* 4.3 0.2 - - - -
366A CYS* 2.8 18.4 + - - +
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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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18A LEU* 5.3 5.4 - - + -
126A SER* 4.2 8.3 - - - +
127A GLY 3.2 1.3 - - - +
128A VAL* 3.7 39.7 - - + -
139A PRO* 3.8 13.4 + - + +
140A SER* 1.3 74.3 - - - +
142A MET* 1.3 59.8 + - - +
143A PRO* 3.3 8.4 - - + +
157A PHE* 3.6 54.5 - - + +
160A ILE* 4.1 15.7 - - + -
161A ALA* 4.5 3.6 - - + +
170A CYS 3.6 5.9 + - - +
171A CYS* 3.4 23.6 - - + +
361A MET* 3.2 16.8 - - - +
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Residues in contact with MET 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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126A SER* 3.2 7.4 + - - -
127A GLY 2.9 27.8 + - - +
129A SER* 3.5 25.4 - - - +
140A SER* 4.5 7.0 - - - +
141A LEU* 1.3 75.7 - - - +
143A PRO* 1.3 65.9 - - - +
144A GLY 3.4 1.4 + - - -
174A VAL* 3.8 7.6 - - + -
180A GLY* 3.5 15.4 - - - +
183A VAL* 3.7 26.2 - - + -
184A LYS* 3.9 28.3 - - + -
187A HIS* 4.2 10.1 - - + -
361A MET* 3.5 20.2 - - + -
362A TRP* 3.3 28.5 - - + +
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Residues in contact with PRO 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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124A VAL* 4.1 3.8 - - + -
126A SER* 3.5 12.8 - - - +
141A LEU 3.3 8.7 - - - +
142A MET* 1.3 85.8 - - - +
144A GLY* 1.3 58.3 + - - +
150A TRP* 3.7 15.7 - - + -
153A ILE* 4.5 0.2 - - + -
157A PHE* 3.5 35.4 - - + -
171A CYS* 3.8 7.4 - - - -
172A ASP 3.5 17.3 - - - +
173A TRP* 3.3 25.2 - - + -
174A VAL* 3.2 25.8 + - - +
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Residues in contact with GLY 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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124A VAL* 3.3 5.6 - - - +
125A GLY 2.6 47.9 + - - -
142A MET 3.4 0.2 + - - -
143A PRO* 1.3 75.0 - - - +
145A GLY* 1.3 55.8 + - - -
173A TRP* 3.5 9.1 - - - -
175A GLY 3.4 12.6 - - - -
178A GLY 4.3 4.3 - - - -
180A GLY 4.2 13.0 - - - -
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Residues in contact with GLY 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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113A CYS* 3.7 11.6 - - - -
123A PHE* 3.8 6.7 - - - -
125A GLY 4.6 1.3 - - - -
144A GLY* 1.3 73.7 - - - -
146A ASN* 1.3 60.9 + - - -
147A LYS 3.9 1.7 + - - -
173A TRP* 3.4 2.4 - - - -
175A GLY 3.1 9.7 + - - -
176A ASP* 2.7 31.7 - - - +
177A GLU 3.1 13.1 + - - -
178A GLY 3.7 9.9 - - - +
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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