Contacts of the helix formed by residues 130 - 134 (chain B) in PDB entry 3L6D
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 TYR 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A PHE* 3.5 29.1 - + - -
221A ASP* 5.0 2.2 - - - -
222A ALA* 4.2 18.4 - - + -
239A GLN* 3.6 15.9 - - - +
240A ALA* 3.8 17.4 - - + +
245A HIS* 2.7 40.5 + + - -
286A ILE* 5.5 0.7 - - + -
20B MSE 4.4 1.1 - - - -
129B ALA* 1.3 79.3 - - - +
131B PRO* 1.4 68.3 - - + +
132B ARG* 3.1 32.3 - - + +
133B ASN* 2.8 30.2 + - - +
134B VAL* 3.5 5.9 + - - +
184B PHE* 3.9 8.1 - + - -
187B MSE 3.7 17.0 - - + +
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Residues in contact with PRO 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLN* 3.7 15.9 - - - +
19B ALA* 4.9 11.7 - - + +
20B MSE 3.8 28.7 - - + +
23B ILE* 3.7 26.9 - - + +
130B TYR* 1.4 91.4 - - + +
132B ARG* 1.3 61.9 + - - +
134B VAL* 3.0 31.1 + - + +
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Residues in contact with ARG 132 (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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221A ASP* 2.8 33.1 + - - -
222A ALA* 4.1 5.5 - - - +
225A GLU* 3.6 42.8 + - - +
239A GLN* 3.1 55.4 + - - +
240A ALA* 5.5 2.0 - - - +
23B ILE* 5.8 2.2 - - - -
130B TYR* 3.0 28.5 + - + +
131B PRO* 1.3 75.5 - - - +
133B ASN* 1.3 72.6 + - - +
134B VAL 3.5 3.4 + - - +
136B HIS* 5.8 0.3 - - - -
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Residues in contact with ASN 133 (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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217A PHE* 4.1 12.1 - - + -
221A ASP* 3.0 39.1 + - - +
129B ALA* 4.3 7.2 - - + -
130B TYR* 2.8 16.5 + - - +
132B ARG* 1.3 97.6 - - - +
134B VAL* 1.3 64.7 + - - -
135B GLY 3.3 0.3 + - - -
136B HIS* 3.1 31.4 + - + -
139B SER* 2.7 36.5 + - - +
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Residues in contact with VAL 134 (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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20B MSE 3.5 32.1 - - + -
23B ILE* 3.7 12.6 - - + +
24B MSE 4.0 25.6 - - + -
27B VAL* 3.5 19.4 - - + +
127B ILE* 4.2 15.7 - - + -
129B ALA* 5.1 0.2 - - + -
130B TYR 4.1 2.7 - - - +
131B PRO* 3.0 21.6 + - + +
132B ARG 4.5 2.9 - - - +
133B ASN* 1.3 79.4 - - - +
135B GLY* 1.3 60.9 + - - +
136B HIS 3.4 1.7 + - - -
160B LEU* 3.6 23.6 - - + +
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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