Contacts of the strand formed by residues 141 - 150 (chain B) in PDB entry 2IT4
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 LEU 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B TYR* 3.9 5.5 + - - -
91B PHE* 4.3 8.3 - - + -
121B ALA* 6.5 0.4 - - + -
122B HIS 3.4 7.2 - - - +
123B TRP* 3.6 21.3 - - + -
131B LEU* 3.8 19.1 - - + -
134B ALA* 4.4 0.9 - - + +
135B ALA* 4.0 22.7 - - + +
139B ASP 3.6 1.5 - - - -
140B GLY* 1.3 84.9 + - - +
142B ALA* 1.3 56.5 + - - +
143B VAL* 5.1 3.4 - - + -
198B LEU* 3.8 25.8 - - + -
206B SER* 2.8 37.3 + - - +
207B VAL* 3.3 10.3 - - + -
208B THR* 2.7 33.1 + - - -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 3.7 15.3 - - + -
84B PHE* 3.3 32.5 - - + -
88B TYR* 3.6 18.7 - - + -
122B HIS* 2.9 42.3 + - - -
141B LEU* 1.3 72.5 - - - +
143B VAL* 1.3 62.8 + - - +
208B THR 3.3 5.4 - - - +
210B ILE* 5.5 0.7 - - + -
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B HIS* 6.0 0.4 - - + -
119B HIS* 3.6 18.8 - - + -
120B VAL 3.4 10.8 - - - +
121B ALA* 4.3 15.5 - - + -
141B LEU* 5.1 3.6 - - + -
142B ALA* 1.3 78.8 - - - +
144B ILE* 1.3 72.2 + - - +
198B LEU* 5.7 3.1 - - + -
207B VAL* 3.4 27.1 - - + +
208B THR 3.2 7.4 + - - -
209B TRP* 3.4 38.3 - - + -
210B ILE* 2.8 26.6 + - - -
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 4.7 7.6 - - + -
49B VAL* 3.8 29.2 - - + -
51B TYR* 4.2 7.0 - - - +
79B LEU* 4.2 14.4 - - + -
118B LEU 3.3 0.9 - - - +
119B HIS* 3.2 6.8 - - - -
120B VAL* 2.8 40.9 + - + +
122B HIS* 4.2 9.0 - - + -
143B VAL* 1.3 76.2 - - - +
145B GLY* 1.3 59.8 + - - +
146B VAL* 4.0 3.8 - - + -
185B LEU* 3.9 35.0 - - + -
189B LEU* 5.7 1.6 - - + -
210B ILE* 3.2 24.7 - - + +
212B CYS* 3.9 18.4 - - - -
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU* 4.5 4.0 - - - -
118B LEU 3.1 7.9 - - - -
119B HIS* 4.0 11.2 - - - -
143B VAL 3.6 2.2 + - - -
144B ILE* 1.3 74.1 - - - +
146B VAL* 1.3 63.1 + - - +
147B LEU* 4.2 0.7 - - - -
209B TRP* 4.3 1.3 - - - -
210B ILE 2.8 9.7 + - - +
211B ILE* 3.4 19.7 - - - +
212B CYS* 2.9 28.6 + - - +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU* 3.5 4.9 - - - +
118B LEU* 2.8 54.1 + - + +
120B VAL* 5.3 0.2 - - + -
144B ILE* 4.0 7.0 - - + -
145B GLY* 1.3 77.7 - - - +
147B LEU* 1.3 73.7 + - - +
148B MET* 3.7 1.0 + - - +
185B LEU* 3.6 31.2 - - + -
186B PRO* 3.8 22.9 - - + -
212B CYS* 4.1 5.2 - - + -
214B GLU 4.1 8.5 - - - +
216B ILE* 3.8 23.1 - - + -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B SER* 3.7 12.3 - - - +
107B HIS* 3.4 31.2 - - + +
109B VAL* 3.8 27.8 - - + -
114B TYR* 3.8 32.3 - - + -
116B ALA 3.9 2.2 - - - -
117B GLU* 3.7 17.3 - - - +
145B GLY 4.4 0.8 + - - -
146B VAL* 1.3 74.2 - - - +
148B MET* 1.3 60.4 + - - +
192B TRP* 5.3 0.4 - - + -
211B ILE* 4.6 11.9 - - + -
212B CYS 4.6 15.1 + - - +
213B LYS 6.0 1.1 - - - +
214B GLU 5.1 1.0 + - - -
215B SER* 3.2 14.6 - - - +
216B ILE* 3.0 26.2 + - - +
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Residues in contact with MET 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PHE* 3.8 25.4 - - + -
114B TYR* 3.3 4.9 - - - +
115B SER* 2.9 26.0 + - - -
116B ALA* 2.8 23.9 + - + +
117B GLU 3.8 10.3 - - - -
118B LEU* 3.7 21.5 - - - -
146B VAL 3.9 4.3 - - - +
147B LEU* 1.3 75.7 - - - +
149B LYS* 1.3 61.5 + - - +
150B VAL 4.1 0.2 - - - -
157B LEU* 3.9 28.5 - - + -
216B ILE* 3.2 29.8 - - + +
217B SER 4.5 0.9 - - - +
218B VAL* 4.0 26.5 - - + -
226B PHE* 4.8 3.4 - - + -
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B TYR* 3.8 28.8 - - + -
115B SER* 4.1 2.2 - - - +
148B MET* 1.3 74.0 - - - +
150B VAL* 1.3 76.0 + - + +
151B GLY 3.2 0.9 + - - -
215B SER* 4.1 11.4 - - - +
216B ILE 2.9 13.3 + - - +
217B SER* 3.4 6.1 - - - -
218B VAL* 3.1 19.4 + - - -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASN* 3.7 24.5 - - + +
102B GLU* 5.4 5.4 - - - +
115B SER* 3.1 27.7 + - - +
149B LYS* 1.3 83.8 - - + +
151B GLY* 1.3 57.6 + - - +
218B VAL* 3.1 16.6 - - - +
219B SER 3.9 0.9 - - - -
220B SER* 3.6 30.3 - - - +
223B LEU* 4.1 4.5 - - + -
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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