Contacts of the helix formed by residues 134 - 139 (chain B) in PDB entry 6F0X
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 GLY 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B HIS* 1.3 89.9 + - - +
135B LEU* 1.3 61.9 + - - +
136B TRP 3.6 1.1 - - - -
137B ASP* 3.8 16.6 + - - +
138B SER* 3.6 15.2 + - - -
167C ASN* 5.6 3.3 - - - +
168C LEU* 5.5 4.0 - - - +
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Residues in contact with LEU 135 (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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132B PHE* 3.1 47.6 + - + +
133B HIS 2.9 3.2 + - - +
134B GLY* 1.3 74.5 - - - +
136B TRP* 1.3 59.4 + - - +
137B ASP 3.1 2.7 - - - -
138B SER* 2.3 51.6 + - - +
139B LEU* 3.2 17.6 + - + +
187B SER* 4.0 21.3 - - - +
190B LYS* 4.9 1.1 - - + -
191B ALA* 3.8 24.7 - - + +
901B AGS 5.5 2.2 - - - +
167C ASN* 4.8 21.3 - - + +
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Residues in contact with TRP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 5.1 12.7 - - + +
132B PHE 4.7 0.8 + - - -
134B GLY 3.6 0.2 - - - -
135B LEU* 1.3 78.0 - - - +
137B ASP* 1.3 73.3 + - - +
139B LEU* 3.3 17.7 + - + +
146B LYS* 3.3 64.3 + - + +
149B LEU* 6.1 2.7 - - + -
150B LEU* 5.2 9.2 - - + +
188B LEU* 4.4 16.6 - - + -
191B ALA* 3.7 34.6 - - + +
192B LEU* 3.9 28.5 - - + -
194B GLN* 6.4 0.4 - - + -
195B LYS* 3.4 42.0 - - + +
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Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B THR* 5.3 6.6 - - - +
74B SER* 4.9 11.8 - - - -
76B ILE* 3.2 33.7 - - + +
134B GLY* 3.8 16.5 + - - +
135B LEU 3.1 0.6 - - - -
136B TRP* 1.3 86.3 - - - +
138B SER* 1.3 64.2 + - - +
139B LEU 3.6 3.8 - - - +
140B VAL* 3.9 8.3 - - - +
146B LYS* 5.2 1.7 + - - +
195B LYS* 5.2 2.4 + - - -
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLY 3.6 8.8 + - - -
135B LEU* 2.3 50.2 + - - +
137B ASP* 1.3 74.2 - - - +
139B LEU* 1.3 67.3 + - - +
140B VAL* 3.2 10.7 + - - +
333B SER* 6.6 0.4 - - - -
389B ARG* 3.2 30.2 + - - +
901B AGS 3.6 2.2 + - - -
167C ASN* 4.4 17.6 + - - -
168C LEU* 4.6 14.8 - - - -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.2 15.0 + - + +
136B TRP* 3.3 17.7 - - + +
137B ASP 3.5 1.2 - - - +
138B SER* 1.3 88.9 + - - +
140B VAL* 1.3 62.9 + - - +
141B TYR* 4.4 6.3 - - + +
146B LYS* 3.6 11.6 + - + +
184B GLY* 5.3 2.2 - - - -
187B SER* 3.7 13.0 - - - +
188B LEU* 3.6 50.0 - - + +
191B ALA* 4.0 12.8 - - + -
901B AGS 3.2 52.3 - - + +
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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