Contacts of the strand formed by residues 140 - 145 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G GLY 3.6 3.8 - - - +
129G SER* 3.4 25.9 + - - -
138G GLY 3.8 2.2 + - - -
139G PRO* 1.3 73.3 - - - +
141G LEU* 1.3 63.6 + - - +
142G MET* 4.6 2.6 - - - +
161G ALA* 5.1 0.2 - - - -
170G CYS 3.9 5.5 + - - -
361G MET* 2.1 39.9 + - - +
364G GLY 3.8 19.8 + - - -
365G GLY* 4.1 2.4 - - - -
366G CYS* 3.5 25.3 - - - -
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Residues in contact with LEU 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G LEU* 5.7 4.0 - - + -
126G SER* 4.0 8.3 - - - +
127G GLY 3.2 3.1 - - - -
128G VAL* 3.6 24.0 - - + -
139G PRO* 3.3 33.2 + - + +
140G SER* 1.3 76.7 + - - +
142G MET* 1.3 65.0 + - - +
143G PRO* 3.5 6.0 - - + +
157G PHE* 3.5 48.5 - - + +
160G ILE* 5.0 6.3 - - + -
161G ALA* 3.8 15.5 - - + -
170G CYS 4.1 4.4 + - - -
171G CYS* 3.5 21.6 - - - +
361G MET* 3.4 18.5 - - - +
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Residues in contact with MET 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G GLY 3.5 4.2 - - - +
126G SER* 3.2 6.8 + - - -
127G GLY* 2.8 30.5 + - - +
129G SER* 4.9 2.5 - - - -
140G SER* 4.6 2.0 - - - +
141G LEU* 1.3 78.9 - - - +
143G PRO* 1.3 65.5 - - - +
144G GLY 3.5 0.2 + - - -
174G VAL* 3.8 5.6 - - + -
180G GLY* 3.7 14.6 - - - +
183G VAL* 4.1 11.2 - - + -
184G LYS* 3.7 41.7 - - + -
187G HIS* 3.8 14.1 - - + -
361G MET* 3.5 22.4 - - + +
362G TRP* 3.7 24.9 - - + -
366G CYS* 3.8 23.1 - - - -
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Residues in contact with PRO 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G VAL* 4.3 7.2 - - + -
126G SER* 3.4 18.6 - - - +
141G LEU 3.5 7.2 - - - +
142G MET* 1.3 87.8 - - - +
144G GLY* 1.3 59.3 + - - +
150G TRP* 3.9 22.4 - - + -
153G ILE* 4.3 2.7 - - + -
157G PHE* 4.3 11.0 - - + -
171G CYS* 4.0 11.7 - - - -
172G ASP 3.3 23.3 - - - +
173G TRP* 3.3 23.5 - - + -
174G VAL* 3.1 19.1 + - - +
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Residues in contact with GLY 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G VAL* 3.5 2.3 - - - +
125G GLY* 2.7 45.9 + - - +
142G MET 3.5 0.2 + - - -
143G PRO* 1.3 74.6 - - - +
145G GLY* 1.3 55.9 + - - -
173G TRP* 3.6 10.6 - - - -
174G VAL* 4.7 0.9 - - - -
175G GLY 3.3 13.9 - - - -
178G GLY* 4.4 7.8 + - - -
180G GLY* 4.2 11.4 - - - -
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Residues in contact with GLY 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G THR* 5.8 0.7 - - - -
113G CYS* 3.2 17.7 - - - -
123G PHE* 3.6 9.4 - - - -
124G VAL* 4.5 0.4 - - - -
125G GLY 4.7 0.4 - - - -
144G GLY* 1.3 75.5 - - - -
146G ASN* 1.3 61.3 + - - +
173G TRP* 3.3 2.4 - - - -
175G GLY 3.2 10.3 + - - -
176G ASP* 3.9 5.2 - - - +
177G GLU* 3.0 29.4 + - - +
178G GLY* 3.5 8.9 - - - +
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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