Contacts of the helix formed by residues 125 - 130 (chain B) in PDB entry 6GYS
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 LEU 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU* 2.6 22.7 + - + +
123B GLY 3.1 0.8 - - - -
124B ALA* 1.3 81.9 - - - +
126B TYR* 1.3 62.4 + - - +
127B PHE 3.1 5.3 + - - -
128B GLY 3.5 6.4 + - - -
129B SER* 4.1 2.8 + - - -
169B MET* 4.4 8.7 - - - -
173B TYR* 3.9 27.1 - - + +
239B ILE* 5.5 0.6 - - - +
242B THR* 3.7 34.5 - - + -
295B ARG* 3.3 27.4 + - - +
398B PHE* 4.1 18.4 - - + -
402B ILE* 3.8 21.5 - - + -
456B HIS* 4.8 10.3 - - + +
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Residues in contact with TYR 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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118B ALA* 3.3 26.2 + - + -
119B MET* 3.3 16.3 + - - +
122B LEU* 3.2 26.5 + - + -
123B GLY* 3.4 18.5 - - - -
125B LEU* 1.3 76.4 - - - +
127B PHE* 1.3 66.3 + - + +
128B GLY 3.3 0.4 - - - -
129B SER* 3.4 3.3 + - - -
130B ILE* 3.1 33.7 + - + +
131B GLY 3.3 25.0 + - - -
133B ILE* 3.3 42.2 - - + +
136B LEU* 5.0 4.5 - - + -
166B VAL* 5.7 5.6 - - + -
169B MET* 4.0 18.4 - - + -
239B ILE* 4.2 20.4 - - + -
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLY* 3.2 22.9 + - - +
124B ALA 5.2 1.3 - - - -
125B LEU 3.1 1.4 - - - +
126B TYR* 1.3 81.3 - - + +
128B GLY* 1.3 63.4 + - - +
130B ILE 3.6 1.0 - - - -
131B GLY* 2.9 47.8 + - - +
291B ARG* 3.0 47.8 + - - -
341B THR* 5.1 7.6 - - - -
342B GLU* 5.4 10.1 - - + -
399B GLN* 6.3 1.3 - - - -
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Residues in contact with GLY 128 (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 ALA 5.6 0.4 + - - -
125B LEU 3.5 7.8 + - - -
126B TYR 3.3 0.2 - - - -
127B PHE* 1.3 82.6 - - - +
129B SER* 1.3 66.1 + - - +
238B LEU* 6.2 0.4 - - - -
288B THR* 4.5 2.9 - - - +
291B ARG* 3.8 35.5 - - - +
292B ILE* 3.8 10.4 + - - +
295B ARG* 4.6 18.0 - - - +
342B GLU* 5.5 4.7 - - - +
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU 4.1 3.2 + - - -
126B TYR* 3.4 10.8 + - - -
127B PHE 3.3 0.6 - - - -
128B GLY* 1.3 80.3 - - - +
130B ILE* 1.3 69.8 + - - +
162B LEU* 4.7 1.2 - - - +
235B GLN* 3.4 47.6 + - - +
238B LEU* 5.2 9.4 - - - -
239B ILE* 3.8 23.8 - - - +
288B THR* 4.4 4.9 - - - +
292B ILE* 3.8 14.6 - - - +
295B ARG* 5.2 2.2 - - - +
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Residues in contact with ILE 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 TYR* 3.1 15.9 + - + +
127B PHE 3.6 1.8 - - - -
129B SER* 1.3 85.9 - - - +
131B GLY* 1.3 66.1 + - - +
132B ASP* 3.2 14.8 + - - +
135B GLU* 5.6 1.4 - - - +
136B LEU* 3.7 46.4 - - + -
159B TRP* 5.7 3.4 - - + -
162B LEU* 4.4 13.7 - - + -
166B VAL* 5.6 2.5 - - + -
235B GLN* 3.3 30.3 - - - +
239B ILE* 6.0 1.3 - - + -
288B THR* 5.3 8.9 - - - +
562C LEU* 6.1 0.2 - - + -
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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