Contacts of the strand formed by residues 141 - 150 (chain B) in PDB entry 1JCZ
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
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Residue Dist Surf HB Arom Phob DC
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88B TYR* 3.7 7.8 + - - -
121B VAL* 4.7 11.2 - - + -
122B HIS 3.4 14.8 - - - +
123B TYR* 3.9 12.8 - - + -
131B ALA* 4.5 6.1 - - + +
135B SER* 4.0 30.1 - - - +
139B GLU* 3.6 1.6 - - - +
140B GLY* 1.3 86.7 - - - +
142B ALA* 1.3 63.1 + - - +
143B VAL* 5.0 2.5 - - + -
198B LEU* 3.5 32.3 - - + -
206B THR* 3.0 30.0 + - - +
207B VAL* 3.9 9.2 - - + -
208B LEU* 2.9 24.9 + - - +
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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 ILE* 4.6 6.5 - - + -
84B LEU* 4.2 14.1 - - + -
88B TYR* 3.3 38.8 - - + -
122B HIS* 2.8 36.9 + - + +
141B LEU* 1.3 73.6 - - - +
143B VAL* 1.3 62.8 + - - +
208B LEU* 3.3 12.8 - - + +
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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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119B HIS* 4.0 15.0 - - + -
120B ILE 3.4 9.4 - - - +
121B VAL* 4.1 16.4 - - + -
141B LEU* 5.0 0.4 - - + -
142B ALA* 1.3 80.2 - - - +
144B LEU* 1.3 73.6 + - - +
145B ALA 4.0 0.3 + - - -
207B VAL* 3.6 18.6 - - + -
208B LEU 3.1 8.3 + - - +
209B TRP* 3.4 32.3 - - + -
210B THR* 3.0 27.7 + - - +
802B ACY 3.4 25.1 - - + -
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Residues in contact with LEU 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 LEU* 4.0 14.6 - - + -
49B PHE* 3.5 20.4 - - + -
51B TYR* 3.4 27.1 - - + +
79B ILE* 3.7 24.0 - - + -
118B LEU 3.4 1.4 - - - +
119B HIS* 3.3 5.5 - - - -
120B ILE* 2.9 49.9 + - + +
122B HIS* 3.9 7.4 - - + -
142B ALA 6.0 0.2 - - - -
143B VAL* 1.3 74.6 - - - +
145B ALA* 1.3 58.1 + - - +
146B VAL* 4.2 1.1 - - + +
185B LEU* 4.6 2.7 - - + -
210B THR* 3.4 26.5 - - + +
212B PHE* 4.1 16.8 - - + -
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Residues in contact with ALA 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* 3.5 24.2 - - - +
118B LEU 3.2 3.8 - - - -
119B HIS* 3.8 8.7 - - + -
143B VAL 4.0 0.2 + - - -
144B LEU* 1.3 74.1 - - - +
146B VAL* 1.3 63.0 + - - +
147B LEU 4.1 0.4 + - - -
209B TRP* 3.9 7.9 - - + -
210B THR 2.8 9.8 + - - +
211B VAL* 3.6 28.4 - - + +
212B PHE* 3.0 30.7 + - - -
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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* 3.3 6.3 - - - +
118B LEU* 2.9 46.7 + - + +
120B ILE* 5.2 1.1 - - + -
144B LEU 5.1 2.2 - - - +
145B ALA* 1.3 77.7 - - - +
147B LEU* 1.3 68.7 + - - +
148B ILE* 3.7 1.8 + - + +
157B TYR* 3.5 21.5 - - - +
184B LEU 3.7 5.4 - - - +
185B LEU* 3.9 28.3 - - + -
186B PRO* 3.8 9.9 - - + -
212B PHE* 4.0 11.4 - - + -
216B VAL* 3.5 27.4 - - + -
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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* 4.4 3.8 - - - -
107B HIS* 4.1 13.7 - - + +
109B VAL* 3.9 16.2 - - + -
114B PHE* 3.7 40.4 - - + -
116B ALA 3.9 2.2 - - - -
117B GLU* 3.7 26.0 - - - +
145B ALA 4.1 0.2 + - - -
146B VAL* 1.3 74.6 - - - +
148B ILE* 1.3 59.3 + - - +
192B TYR* 5.6 0.4 - - + -
211B VAL* 4.3 18.8 - - + -
212B PHE 3.9 18.3 + - - +
213B ARG* 4.4 8.1 - - - +
214B ASN 5.0 1.4 + - - -
215B PRO* 3.1 18.9 - - + +
216B VAL* 2.9 28.1 + - - +
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Residues in contact with ILE 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 LEU* 3.7 29.6 - - + -
114B PHE* 3.4 5.0 - - - +
115B ALA* 2.9 26.2 + - + +
116B ALA* 2.9 34.4 + - + +
118B LEU* 4.1 9.9 - - + +
146B VAL 3.8 6.7 - - - +
147B LEU* 1.3 78.9 - - - +
149B GLU* 1.3 64.6 + - - +
157B TYR* 3.9 18.4 - - + +
161B PHE* 5.7 1.8 - - + -
216B VAL* 3.6 17.5 - - + +
218B ILE* 3.7 43.3 - - + -
226B LEU* 5.9 0.2 - - + -
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Residues in contact with GLU 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 PHE* 3.9 18.7 - - + -
115B ALA* 4.1 8.3 - - - +
148B ILE* 1.3 77.4 - - - +
150B MET* 1.3 68.0 + - - +
215B PRO* 3.6 26.6 - - + +
216B VAL 3.0 18.9 + - - +
217B GLN* 3.2 29.3 + - + +
218B ILE* 3.1 24.8 + - - +
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Residues in contact with MET 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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115B ALA* 4.3 6.0 - - + +
149B GLU* 1.3 80.9 - - - +
151B GLY* 1.3 74.3 + - - +
217B GLN* 4.7 1.4 - - - +
218B ILE* 3.3 7.6 - - - +
219B SER 4.2 0.4 - - - +
220B GLN* 3.2 61.9 - - + +
223B LEU* 4.3 17.5 - - + -
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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