Contacts of the strand formed by residues 133 - 142 (chain g) in PDB entry 5K0Y
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 GLY 133 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127g MET* 4.0 7.2 - - - -
131g ALA* 3.2 5.2 - - - +
132g LYS* 1.4 81.1 - - - +
134g CYS* 1.3 64.9 + - - +
154g ASP 3.5 10.3 - - - -
155g GLY* 3.9 2.5 - - - -
156g LEU 3.3 18.5 + - - -
157g MET* 4.0 2.7 - - - -
189g MET* 2.9 26.2 + - - +
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Residues in contact with CYS 134 (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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123g LEU* 3.5 26.6 - - - +
126g ILE* 3.7 31.9 - - + -
127g MET* 3.8 23.6 - - - -
131g ALA* 4.9 0.9 - - - -
133g GLY* 1.3 76.6 - - - +
135g GLU* 1.4 61.3 + - - +
153g VAL* 3.7 2.5 - - - +
154g ASP* 2.9 35.5 + - - +
156g LEU 4.4 0.4 + - - -
157g MET* 3.7 6.9 - - - +
187g LYS 3.3 13.9 - - - +
188g ILE* 4.3 6.5 - - + -
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Residues in contact with GLU 135 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1481A U 5.2 0.3 + - - -
123g LEU* 4.4 0.4 - - - -
134g CYS* 1.4 75.1 - - - +
136g VAL* 1.3 67.8 + - - +
137g VAL* 4.3 12.0 - - + +
151g LYS* 3.6 24.9 + - - +
152g PHE 3.5 5.6 - - - -
153g VAL* 3.9 22.3 - - + +
157g MET* 3.6 20.8 - - + +
159g HIS* 4.4 8.9 + - - -
185g LYS* 4.0 1.6 - - - +
186g VAL* 3.8 0.2 - - - -
187g LYS* 3.0 73.3 + - + +
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Residues in contact with VAL 136 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105g LEU* 3.6 29.4 - - + -
119g CYS* 4.4 19.1 - - + +
122g VAL* 5.3 3.1 - - + -
123g LEU* 3.9 25.8 - - + +
126g ILE* 4.6 5.6 - - + -
135g GLU* 1.3 79.0 - - - +
137g VAL* 1.4 72.2 + - - +
138g VAL* 4.5 1.1 - - + -
152g PHE* 3.0 42.0 + - + +
184g ILE* 5.0 0.2 - - + -
185g LYS 3.5 7.9 - - - +
186g VAL* 4.4 20.2 - - + -
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Residues in contact with VAL 137 (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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1331A G 5.9 0.7 - - - +
135g GLU* 4.3 19.1 - - + +
136g VAL* 1.4 80.9 - - - +
138g VAL* 1.4 73.1 + - - +
139g SER* 4.1 10.5 - - - +
149g SER* 4.9 5.8 - - - -
150g MET 3.5 16.6 - - - +
151g LYS* 4.4 21.8 - - + +
183g GLY 3.5 2.8 - - - +
184g ILE* 3.6 2.8 - - - -
185g LYS* 3.0 47.5 + - + +
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Residues in contact with VAL 138 (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 LEU* 5.3 3.6 - - + -
115g VAL* 4.5 10.3 - - + -
119g CYS* 3.6 31.0 - - - -
136g VAL* 4.3 5.1 - - + -
137g VAL* 1.4 78.5 - - - +
139g SER* 1.4 67.4 - - - +
148g LYS 4.3 0.2 - - - +
149g SER* 3.6 2.4 - - - -
150g MET* 3.2 49.5 + - + +
152g PHE* 4.4 5.2 - - + -
182g LEU* 4.8 16.6 - - + -
183g GLY 3.4 3.6 - - - +
184g ILE* 3.9 24.5 - - + -
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Residues in contact with SER 139 (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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1330A G 3.9 7.8 + - - +
1331A G 3.7 33.3 + - - -
137g VAL* 4.6 10.1 - - - -
138g VAL* 1.4 74.9 - - - +
140g GLY* 1.4 60.9 + - - +
148g LYS 3.8 5.7 + - - -
149g SER* 3.4 17.4 + - - -
182g LEU* 3.5 10.2 - - - +
183g GLY 3.0 30.2 + - - -
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Residues in contact with GLY 140 (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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1329A U 3.6 6.7 - - - -
1330A G 3.4 25.3 + - - -
139g SER* 1.4 80.0 + - - +
141g LYS* 1.3 61.6 + - - -
147g ALA* 4.2 3.5 - - - +
148g LYS* 2.8 31.4 + - - +
182g LEU* 3.9 5.6 - - - -
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Residues in contact with LYS 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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618A A 3.2 35.0 + - - +
1328A A 3.3 22.6 + - + +
1329A U 3.8 37.6 + - - +
140g GLY* 1.3 73.4 - - - -
142g LEU* 1.3 69.3 + - - +
144g GLY* 3.6 24.5 + - - +
146g ARG 3.7 14.8 - - - +
147g ALA* 4.3 1.6 - - - +
179g GLN* 3.4 45.4 + - + +
180g GLY* 4.8 2.7 - - - -
182g LEU* 3.3 26.0 - - + +
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Residues in contact with LEU 142 (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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20F C 5.5 1.3 - - - +
115g VAL* 5.1 21.3 - - + -
140g GLY 4.1 1.0 + - - -
141g LYS* 1.3 79.7 - - - +
143g ARG* 1.4 93.6 + - + +
144g GLY 3.4 3.3 - - - +
146g ARG 3.2 11.9 + - - +
148g LYS* 3.2 39.3 + - + +
150g MET* 5.8 9.0 - - + -
179g GLN* 4.6 15.9 - - - +
182g LEU* 5.3 10.3 - - + -
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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