Contacts of the strand formed by residues 155 - 161 (chain B) in PDB entry 1LT8
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 PHE 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 3.4 49.1 - - + -
70B VAL* 4.0 14.1 - - + -
117B LEU* 4.5 8.7 - - + -
118B VAL 3.5 3.0 + - - -
119B ALA* 3.4 17.9 - - + -
120B GLY 3.0 22.9 + - - -
153B VAL* 3.5 5.9 - - - +
154B ASP* 1.3 88.4 - - + +
156B LEU* 1.3 74.5 + - - +
157B ILE* 3.6 23.3 - - + -
179B LYS* 4.2 6.1 - - - -
180B PRO* 3.3 17.0 - - + +
182B ALA* 4.3 8.7 - - + -
212B ILE* 5.1 2.0 - - + -
295B TYR* 3.8 30.7 - + - -
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Residues in contact with LEU 156 (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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120B GLY 3.1 17.5 - - - +
122B VAL* 5.7 0.7 - - + -
145B LEU* 3.6 19.5 - - + -
148B PHE* 3.8 34.3 - - + -
153B VAL* 4.1 7.9 - - + -
155B PHE* 1.3 82.3 - - - +
157B ILE* 1.3 65.0 + - - +
158B ALA 4.2 0.2 - - - -
174B LEU* 3.8 27.4 - - + +
177B SER* 3.4 26.2 - - - +
179B LYS* 4.1 10.3 - - + -
180B PRO 2.9 10.6 + - - +
181B VAL* 4.3 10.1 - - + -
182B ALA 2.8 25.3 + - - -
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Residues in contact with ILE 157 (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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72B GLN* 3.6 26.2 - - + +
119B ALA* 3.5 26.9 - - + -
120B GLY 2.7 11.4 + - - +
121B GLY* 3.2 5.2 - - - -
122B VAL* 2.9 27.0 + - - +
155B PHE* 3.6 17.0 - - + -
156B LEU* 1.3 81.3 - - - +
158B ALA* 1.3 63.1 + - - +
159B GLU* 3.1 32.1 + - + +
174B LEU* 4.6 3.1 - - - +
182B ALA* 3.3 12.3 - - + +
184B THR* 4.9 3.8 - - - +
245B MET* 4.7 13.2 - - + -
295B TYR* 3.9 11.0 - - - +
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Residues in contact with ALA 158 (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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122B VAL* 3.6 7.2 - - - -
157B ILE* 1.3 69.2 - - - +
159B GLU* 1.3 58.1 + - - +
161B PHE* 3.3 24.0 - - + -
167B ALA 4.7 1.1 - - - +
170B ALA* 4.3 4.3 - - + -
171B VAL* 4.2 11.9 - - + -
174B LEU* 4.0 17.2 - - + +
181B VAL* 4.8 0.2 - - + -
182B ALA 2.7 14.7 + - - +
183B ALA* 3.5 14.5 - - + -
184B THR* 3.2 28.4 + - - +
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Residues in contact with GLU 159 (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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72B GLN* 2.9 24.4 + - - -
76B PHE* 4.3 9.1 - - + +
121B GLY* 5.4 3.4 - - - -
122B VAL 2.6 17.6 + - - +
123B SER* 2.8 30.5 - - - -
124B GLN 3.4 1.2 + - - -
157B ILE* 3.1 17.7 + - + +
158B ALA* 1.3 74.7 - - - +
160B TYR* 1.3 72.9 + - + +
161B PHE* 3.3 4.7 - - - -
184B THR* 4.3 4.1 + - - +
216B ASN* 3.2 17.9 + - - +
247B GLN* 3.5 17.0 + - - -
299B CYS* 6.0 0.2 - - - -
602B CBH 2.5 37.5 + - + +
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Residues in contact with TYR 160 (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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340A LYS* 4.9 8.8 + - - -
76B PHE* 3.6 29.4 - + + -
77B TYR* 4.0 16.6 - + - -
123B SER* 4.0 0.9 - - - -
124B GLN* 3.3 38.8 + - + +
159B GLU* 1.3 85.6 - - + +
161B PHE* 1.3 58.7 + - - +
162B GLU* 4.9 2.2 - - - -
184B THR 3.9 0.6 + - - -
186B ALA* 4.0 7.4 - - + -
216B ASN* 3.4 17.0 + - - +
217B CYS* 3.7 14.1 - - + -
218B HIS* 3.0 40.3 - + - -
262B ILE* 4.2 3.5 - - - +
602B CBH 3.0 50.3 - - + +
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Residues in contact with PHE 161 (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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122B VAL* 3.5 6.1 - - + -
123B SER 3.6 12.1 - - - -
124B GLN* 3.2 31.2 - - + +
141B PHE* 3.6 18.6 - + - -
158B ALA* 3.3 25.8 - - + -
159B GLU 3.3 32.7 - - - -
160B TYR* 1.3 74.3 - - - +
162B GLU* 1.3 61.1 + - - +
163B HIS 3.4 3.4 - - - +
166B GLU* 3.8 20.0 - - + -
167B ALA* 3.6 30.1 - - + -
170B ALA* 3.6 18.6 - - + -
184B THR 4.0 6.2 + - - +
185B MET* 3.4 15.3 - - - +
186B ALA 2.8 25.0 + - - +
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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