Contacts of the strand formed by residues 132 - 141 (chain L) in PDB entry 2IG2
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 ALA 132 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122L PRO* 4.0 18.6 - - + -
126L GLU* 3.9 0.7 - - - -
127L LEU* 4.3 1.1 - - + -
131L LYS* 1.3 76.6 - - - +
133L THR* 1.3 65.8 + - - +
134L LEU 3.9 1.3 + - - -
180L LEU 3.8 0.7 - - - +
181L SER* 3.7 0.7 - - - -
182L LEU* 3.0 57.2 + - + +
183L THR 3.7 13.5 - - - +
184L PRO* 3.8 5.6 - - + -
187L TRP* 4.3 4.7 - - + -
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Residues in contact with THR 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H LEU* 5.3 1.2 - - - +
146H LEU* 4.0 14.2 - - + +
148H LYS* 3.5 18.6 + - + -
121L PRO 3.9 2.4 - - - +
122L PRO* 3.5 20.7 - - - +
123L SER 4.9 0.3 + - - -
126L GLU* 2.7 32.2 + - - +
131L LYS* 5.4 0.2 - - - +
132L ALA* 1.3 76.0 + - - +
134L LEU* 1.3 64.0 + - - +
135L VAL* 3.7 25.4 + - + +
179L TYR* 4.1 15.9 - - + -
180L LEU 3.6 7.2 + - - +
181L SER* 4.5 9.4 - - - +
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Residues in contact with LEU 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119L LEU* 4.6 5.2 - - + -
120L PHE 3.6 5.6 - - - +
121L PRO* 3.6 20.4 - - + -
122L PRO* 3.9 4.9 - - + -
132L ALA 3.9 1.0 + - - -
133L THR* 1.3 72.7 - - - +
135L VAL* 1.3 60.5 + - - +
150L TRP* 3.8 16.4 - - + -
178L SER 4.0 0.3 - - - +
179L TYR* 3.5 4.2 - - - -
180L LEU* 2.9 51.7 + - + +
182L LEU* 3.4 30.3 - - + -
187L TRP* 3.5 28.5 - - + -
193L TYR* 3.7 13.9 - - + -
208L VAL* 3.6 17.9 - - + -
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Residues in contact with VAL 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H LEU* 4.4 18.4 - - + -
146H LEU* 4.1 13.2 - - + -
184H SER* 3.8 11.9 - - - +
118L THR 4.3 0.5 - - - +
119L LEU* 3.3 4.0 - - - +
120L PHE* 2.8 42.1 + - + +
133L THR* 3.8 16.4 - - + +
134L LEU* 1.3 79.7 - - - +
136L CYS* 1.3 60.1 + - - +
137L LEU* 4.0 22.3 + - + -
178L SER 3.9 2.0 - - - -
179L TYR* 3.5 40.2 - - + -
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Residues in contact with CYS 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L VAL* 3.9 18.8 - - - -
118L THR 3.9 3.8 - - - -
119L LEU* 4.0 4.5 - - + -
135L VAL* 1.3 72.6 - - - +
137L LEU* 1.3 66.6 + - - +
138L ILE* 4.6 5.7 - - - +
148L VAL* 4.6 2.2 - - - -
150L TRP* 3.5 17.7 - - + -
177L SER* 3.3 4.2 - - - -
178L SER* 2.8 39.8 + - - +
195L CYS* 2.0 51.6 - - + -
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Residues in contact with LEU 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H LEU* 5.2 0.4 - - + -
171H PHE* 3.6 31.0 - - + -
184H SER* 4.2 12.3 - - - -
186H VAL* 3.2 31.6 - - + -
117L VAL* 3.3 5.5 - - - +
118L THR* 2.8 50.2 + - + +
120L PHE* 3.7 24.5 - - + -
135L VAL* 4.0 20.4 - - + -
136L CYS* 1.3 76.5 - - - +
138L ILE* 1.3 64.1 + - - +
139L SER 4.2 0.2 - - - -
176L ALA 3.9 0.7 - - - -
177L SER* 3.7 23.1 - - - +
179L TYR* 4.7 0.7 - - - +
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Residues in contact with ILE 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H PHE* 3.6 4.4 - - - -
115L PRO* 3.6 21.3 - - + -
116L THR 5.0 0.2 - - - +
117L VAL* 4.5 3.6 - - + +
136L CYS* 4.6 12.1 - - - +
137L LEU* 1.3 79.8 - - - +
139L SER* 1.3 58.9 + - - +
141L PHE* 3.3 26.7 - - + -
146L VAL* 4.4 7.0 - - + -
148L VAL* 3.2 38.4 - - + -
175L ALA* 3.5 4.2 - - - -
176L ALA* 2.8 58.7 + - + +
177L SER 4.6 4.0 - - - +
197L VAL* 3.9 18.8 - - + -
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Residues in contact with SER 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H HIS* 4.2 13.3 - - - -
171H PHE* 3.4 21.4 - - - -
115L PRO* 3.4 3.6 - - - +
116L THR* 2.9 42.4 + - - +
118L THR* 4.6 6.2 - - - +
138L ILE* 1.3 78.8 + - - +
140L ASP* 1.3 82.6 - - - +
141L PHE* 3.1 5.9 + - - -
174L TYR 3.8 3.4 - - - -
175L ALA* 4.8 3.1 - - - +
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Residues in contact with ASP 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H HIS* 5.2 0.7 + - - -
113L ALA* 3.6 13.0 - - - +
114L ASN 3.1 14.0 - - - +
116L THR* 3.5 19.0 + - - +
139L SER* 1.3 83.4 - - - +
141L PHE* 1.3 58.2 + - - +
169L GLN* 3.3 20.4 + - - -
171L ASN* 2.9 34.0 + - - +
173L LYS* 3.9 11.2 + - + +
174L TYR 3.5 7.4 + - - -
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Residues in contact with PHE 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L ALA 3.3 10.8 - - - +
115L PRO* 3.6 20.2 - - + -
138L ILE* 3.3 45.1 - - + -
139L SER 3.1 6.5 + - - -
140L ASP* 1.3 79.8 - - - +
142L TYR* 1.3 58.7 + - - +
143L PRO 3.6 11.0 - - - -
144L GLY* 4.1 6.5 - - - -
145L ALA 4.4 0.2 - - - -
146L VAL* 3.2 38.6 - - + -
166L PRO* 3.9 15.0 - - + -
173L LYS* 3.1 4.1 - - - +
174L TYR* 2.6 69.2 + - + +
175L ALA 3.9 6.3 - - - -
176L ALA 3.7 4.3 - - - -
199L HIS* 4.0 2.0 - + - +
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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