Contacts of the strand formed by residues 133 - 143 (chain M) in PDB entry 1I9R
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 133 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148K LYS* 4.3 20.9 + - - +
128M GLN* 2.7 48.1 + - - +
129M LEU* 3.7 3.6 + - - -
131M SER* 2.9 17.1 + - - -
132M GLY* 1.3 79.2 - - - +
134M ALA* 1.3 61.3 + - - +
184M THR* 4.7 10.8 - - - +
185M LEU 4.2 8.1 - - - +
186M SER* 5.4 1.6 - - - -
187M LYS* 4.1 2.0 - - - +
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Residues in contact with ALA 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124M PRO* 4.0 5.4 - - + -
128M GLN* 3.7 1.3 - - - +
129M LEU* 3.5 18.2 - - + -
133M THR* 1.3 74.2 - - - +
135M SER* 1.3 60.2 + - - +
136M VAL* 4.2 1.1 + - - +
184M THR* 3.6 1.4 - - - -
185M LEU* 2.7 42.1 + - - +
187M LYS* 3.9 3.5 - - - +
190M TYR* 3.3 43.0 - - + -
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Residues in contact with SER 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K LEU* 3.6 16.5 - - - +
148K LYS* 4.7 8.1 - - - -
122M PHE 4.7 0.3 - - - +
123M PRO 4.8 0.3 - - - -
124M PRO* 4.0 14.0 - - - +
128M GLN* 2.9 32.3 + - - +
134M ALA* 1.3 75.3 - - - +
136M VAL* 1.3 60.6 + - - +
137M VAL* 3.9 3.6 + - - +
182M THR* 4.2 11.7 - - - -
183M LEU 3.4 8.7 - - - -
184M THR* 3.5 19.7 - - - +
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Residues in contact with VAL 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M ILE* 4.0 13.5 - - + -
122M PHE 3.1 20.0 - - - +
124M PRO* 4.1 12.8 - - + +
134M ALA 4.2 1.3 - - - +
135M SER* 1.3 71.8 - - - +
137M VAL* 1.3 60.0 + - - +
152M TRP* 3.2 27.0 - - + -
182M THR* 3.5 0.4 - - - -
183M LEU* 2.7 74.8 + - + -
184M THR* 5.5 0.2 - - - -
190M TYR* 5.7 2.7 - - + -
196M TYR* 4.8 8.5 - - + -
213M PHE* 4.0 11.9 - - + -
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Residues in contact with VAL 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129K LEU* 4.2 28.0 - - + -
146K LEU* 4.5 9.9 - - + -
184K SER* 4.5 13.9 - - - +
186K VAL* 6.0 2.7 - - + -
121M ILE* 3.6 0.7 - - - +
122M PHE* 2.7 50.6 + - + +
135M SER 3.9 2.6 + - - +
136M VAL* 1.3 73.9 - - - +
138M CYS* 1.3 72.5 + - - +
139M LEU* 4.8 4.5 - - + -
180M SER* 5.0 9.0 - - - -
181M SER 3.8 4.5 - - - +
182M THR* 3.4 29.4 - - + +
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Residues in contact with CYS 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M VAL* 5.1 2.2 - - - -
120M PHE 3.5 6.1 - - - -
121M ILE* 4.2 4.5 - - + +
137M VAL* 1.3 79.8 - - - +
139M LEU* 1.3 64.2 + - - +
140M LEU* 3.8 19.7 - - - +
150M VAL* 4.0 8.1 - - - -
152M TRP* 3.5 13.4 - - + -
180M SER* 3.7 1.4 - - - -
181M SER* 3.0 30.6 + - - +
198M CYS* 2.1 55.0 - - + -
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Residues in contact with LEU 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K ALA* 4.1 5.2 - - + -
169K HIS* 5.8 0.7 - - + -
171K PHE* 3.8 23.3 - - + -
186K VAL* 3.5 32.1 - - + -
188K THR* 5.3 1.3 - - + -
118M SER 3.4 1.7 - - - +
119M VAL* 3.0 4.4 - - - -
120M PHE* 2.7 58.8 + - + +
122M PHE* 4.1 18.4 - - + -
137M VAL* 4.8 4.9 - - + -
138M CYS* 1.3 77.2 - - - +
140M LEU* 1.3 74.5 + - - +
141M ASN* 4.2 13.7 - - + +
178M SER* 4.9 0.4 - - - -
179M LEU 3.6 12.3 - - - +
180M SER* 5.3 0.9 - - - -
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Residues in contact with LEU 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M PRO* 4.0 11.4 - - + -
118M SER 3.8 4.3 - - - -
119M VAL* 4.0 13.0 - - + +
138M CYS* 3.8 22.4 - - - -
139M LEU* 1.3 79.5 - - - +
141M ASN* 1.3 59.7 + - - +
143M PHE* 3.2 18.8 - - + -
148M ALA* 4.4 14.8 - - + -
150M VAL* 3.9 24.7 - - + -
178M SER* 3.1 24.4 - - - -
179M LEU* 3.1 21.8 + - + +
200M VAL* 3.5 32.5 - - + -
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Residues in contact with ASN 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K HIS* 2.5 36.4 + - - -
188K THR* 3.4 25.7 + - + +
116M ALA 4.4 0.2 - - - +
117M PRO* 3.5 2.8 - - - +
118M SER* 2.9 46.0 + - - +
120M PHE* 3.9 14.4 - - + -
139M LEU* 3.6 9.0 + - + +
140M LEU* 1.3 73.1 - - - +
142M ASN* 1.3 91.9 + - - +
143M PHE 3.2 1.5 + - - -
178M SER* 2.6 23.8 + - - -
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Residues in contact with ASN 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K HIS* 2.7 27.1 + - - -
188K THR* 5.3 0.2 + - - -
115M ALA* 4.3 7.1 - - - +
116M ALA 3.8 8.5 - - - +
118M SER* 5.7 0.2 - - - +
141M ASN* 1.3 107.4 - - - +
143M PHE* 1.3 59.4 + - - +
171M ASP* 3.6 4.9 + - - -
174M ASP* 3.0 18.7 + - - +
176M THR* 2.9 30.5 + - + +
177M TYR 2.9 9.1 + - - -
178M SER* 3.1 5.3 + - - -
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Residues in contact with PHE 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M ALA* 3.5 11.2 - - - +
116M ALA 4.2 0.7 - - - -
117M PRO* 3.2 25.4 - - + -
140M LEU* 3.2 28.5 - - + -
142M ASN* 1.3 73.6 - - - +
144M TYR* 1.3 61.8 + - - +
145M PRO 3.4 23.8 - - - -
146M ARG* 4.0 11.0 - - + -
148M ALA* 3.9 20.2 - - + -
167M VAL* 5.2 2.5 - - + -
176M THR* 3.1 3.7 - - - -
177M TYR* 2.6 59.3 + - + -
178M SER* 3.3 4.5 - - - -
179M LEU* 3.0 46.9 - - + -
202M HIS* 3.9 10.8 - + - +
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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