Contacts of the strand formed by residues 151 - 157 (chain B) in PDB entry 4L2A
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 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B VAL* 3.3 3.0 - - - -
127B LYS* 2.7 67.7 + - - -
149B GLY 4.1 1.6 - - - -
150B VAL* 1.3 71.5 + - - +
152B PRO* 1.3 80.7 - - + +
153B ILE* 3.2 4.1 - - + +
190B ASN* 3.7 21.5 - - + +
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Residues in contact with PRO 152 (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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71B TRP* 3.8 23.3 - - + -
75B PHE* 3.4 29.0 - - + -
124B TRP* 4.4 2.7 - - + -
126B VAL* 4.1 11.6 - - + -
144B PRO* 3.9 24.7 - - + -
145B LEU* 4.2 15.0 - - + +
150B VAL 3.7 4.9 - - - +
151B THR* 1.3 94.9 - - + +
153B ILE* 1.3 60.4 + - - +
190B ASN* 3.7 7.1 - - - +
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Residues in contact with ILE 153 (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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75B PHE* 3.6 5.6 - - - -
92B VAL* 4.4 7.0 - - + -
125B LEU* 2.9 44.0 + - + -
126B VAL 3.9 2.2 - - - -
127B LYS* 3.7 23.8 - - + +
133B LEU* 4.5 6.7 - - + -
151B THR* 3.2 20.9 - - + +
152B PRO* 1.3 77.2 - - - +
154B LEU* 1.3 73.5 + - + +
186B PHE* 4.1 0.9 - - - -
187B ALA* 3.1 45.8 - - + +
190B ASN* 3.0 26.2 - - + +
191B PHE* 4.8 8.3 - - + -
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Residues in contact with LEU 154 (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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75B PHE* 3.6 4.4 - - - -
79B SER* 3.6 31.4 - - - +
106B PHE* 6.1 0.9 - - + -
124B TRP* 3.5 6.9 - - - +
125B LEU* 2.9 38.5 + - + +
153B ILE* 1.3 91.8 - - + +
155B THR* 1.3 61.2 + - - +
178B PHE* 4.8 8.1 - - + -
179B TRP* 6.3 0.4 - - + -
182B VAL* 3.5 27.6 - - + -
183B ASN 3.6 21.1 - - - +
184B TRP* 3.8 13.5 - - + -
186B PHE* 4.2 2.0 - - + -
187B ALA* 3.8 22.2 - - + +
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Residues in contact with THR 155 (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 ASN 4.0 3.6 - - - +
75B PHE* 4.0 5.6 - - + -
76B TYR* 3.5 43.0 - - + +
79B SER* 3.1 22.2 + - - -
122B TRP* 3.6 20.7 - - + +
123B THR 3.4 7.6 + - - -
124B TRP* 3.2 38.7 - - + -
154B LEU* 1.3 74.5 - - - +
156B VAL* 1.3 67.1 + - - +
178B PHE* 3.8 8.1 - - - -
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Residues in contact with VAL 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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76B TYR* 4.1 2.5 - - + -
110B LEU* 4.3 18.6 - - + -
114B ALA* 4.7 2.9 - - + -
122B TRP* 3.5 4.8 - - - -
123B THR* 2.8 59.2 + - - +
155B THR* 1.3 76.2 + - - +
157B ASP* 1.3 65.6 + - - +
158B LEU* 3.3 11.4 + - + +
174B TYR* 3.5 31.0 - - + +
175B LEU* 4.4 6.7 - - + -
178B PHE* 3.9 31.2 - - + -
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Residues in contact with ASP 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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26B HIS* 2.8 11.6 + - - -
73B HIS* 3.3 2.8 + - - -
76B TYR* 3.4 27.8 - - + -
122B TRP* 3.4 29.0 - - + -
156B VAL* 1.3 71.5 - - - +
158B LEU* 1.3 59.9 + - - +
159B TRP* 3.1 34.2 + - - -
162B ALA* 3.7 12.0 - - + +
174B TYR* 2.6 32.4 + - - -
5001B FE 2.0 31.3 - - - -
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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