Contacts of the helix formed by residues 124 - 130 (chain B) in PDB entry 4LT6
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 GLU 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B LYS* 5.6 4.4 + - - +
121B ARG 4.4 2.2 - - - +
122B HIS 5.8 1.0 - - - -
123B VAL* 1.3 83.2 - - - +
125B ARG* 1.3 62.4 + - + +
126B SER* 2.8 30.5 + - - +
127B ASP* 2.9 21.9 + - - +
128B PHE 3.3 7.6 + - - -
169B PHE* 4.0 3.5 - - - -
171B ARG* 3.1 39.0 + - - +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU* 1.3 76.0 - - + +
126B SER* 1.3 58.3 + - - +
128B PHE* 3.8 2.1 - - - +
129B PHE* 2.9 40.6 + - - -
149B GLU* 4.8 2.2 + - - +
154B PRO* 3.5 34.1 - - - +
169B PHE* 2.7 56.8 + - + +
171B ARG* 5.1 2.9 - - + -
193B ASP* 4.7 1.8 - - - -
195B ARG* 3.9 52.9 + - - +
196B CYS* 3.5 36.6 - - - +
199B SER* 3.1 15.8 + - - -
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Residues in contact with SER 126 (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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124B GLU* 2.8 14.3 - - - +
125B ARG* 1.3 75.8 - - - +
127B ASP* 1.3 76.0 + - - -
128B PHE 3.0 4.3 - - - -
129B PHE* 2.8 22.2 + - - +
130B GLN* 2.9 27.9 + - - +
149B GLU* 5.9 1.3 - - - -
195B ARG* 5.8 0.2 - - - +
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Residues in contact with ASP 127 (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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74B TRP* 3.4 7.4 - - + -
78B VAL* 3.8 13.8 - - + +
82B LYS* 3.6 22.1 + - - -
123B VAL* 3.7 12.5 - - + -
124B GLU* 2.9 26.1 + - - +
126B SER* 1.3 90.4 + - - +
128B PHE* 1.3 56.6 + - - +
130B GLN* 4.0 14.2 + - - -
131B SER* 2.8 32.0 + - - +
132B PHE 3.1 13.9 + - - -
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 3.8 17.0 - + + -
117B CYS* 4.5 7.4 - - + -
124B GLU 3.3 4.5 + - - +
125B ARG 3.8 6.1 - - - +
126B SER 3.0 0.6 - - - -
127B ASP* 1.3 79.5 - - - +
129B PHE* 1.3 83.8 + + - +
130B GLN 3.4 0.2 - - - -
132B PHE* 3.5 18.8 - + - +
133B PHE 3.4 19.1 + - - -
154B PRO 5.3 0.4 - - - -
155B VAL 5.3 0.2 - - - -
156B ILE* 3.5 36.2 - - + +
167B LEU* 3.9 39.9 - - + -
168B VAL* 5.0 0.2 - - - -
169B PHE* 3.4 57.9 - + + -
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Residues in contact with PHE 129 (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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125B ARG* 2.9 31.4 - - - +
126B SER* 2.8 9.6 + - - +
128B PHE* 1.3 100.2 - + - +
130B GLN* 1.3 58.6 + - - +
133B PHE* 3.5 18.0 - - - +
147B ALA* 4.2 18.2 - - + -
148B VAL 4.1 11.0 - - - -
149B GLU* 3.6 45.5 - - + +
154B PRO* 3.6 32.5 - - + -
155B VAL 3.9 8.1 - - - -
156B ILE* 4.0 19.7 - - + -
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Residues in contact with GLN 130 (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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126B SER* 2.9 29.5 + - - +
127B ASP* 4.0 18.2 + - - -
129B PHE* 1.3 77.1 - - - +
131B SER* 1.3 63.6 + - - +
132B PHE 3.3 1.6 - - - -
133B PHE* 2.9 6.6 + - - +
134B GLU* 2.8 41.9 + - + +
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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