Contacts of the helix formed by residues 124 - 130 (chain I) 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 ALA 124 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122I LEU 2.9 1.6 + - - -
123I GLY* 1.3 78.7 - - - +
125I LEU* 1.3 60.6 + - + +
127I PHE* 3.6 10.9 - - + +
128I GLY* 2.5 32.8 + - - -
295I ARG* 5.0 2.9 + - - -
342I GLU* 5.2 5.3 - - - +
395I ASN* 3.8 8.2 - - + +
398I PHE* 4.9 7.6 - - + -
399I GLN* 3.6 39.3 - - + +
402I ILE* 6.3 0.4 - - + -
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Residues in contact with LEU 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I LEU* 3.1 15.3 + - + +
124I ALA* 1.3 75.2 - - + +
126I TYR* 1.3 55.5 + - - +
128I GLY* 3.1 3.3 + - - -
129I SER* 2.7 32.7 + - - -
169I MET* 4.0 23.1 - - - -
173I TYR* 3.8 22.4 - - + +
239I ILE* 4.6 3.7 - - + +
242I THR* 5.1 13.5 - - + -
295I ARG* 4.3 24.8 + - - +
398I PHE* 3.6 38.8 - - + -
402I ILE* 4.6 9.4 - - + -
456I HIS* 5.4 7.9 - - + +
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Residues in contact with TYR 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I ALA* 3.4 17.7 - - + -
119I MET* 2.8 25.1 + - - +
122I LEU* 3.2 28.0 - - + -
123I GLY* 3.5 9.2 - - - -
125I LEU* 1.3 75.7 - - - +
127I PHE* 1.3 60.9 + - + +
129I SER* 2.9 8.2 + - - -
130I ILE* 2.4 49.1 + - + -
131I GLY 2.7 38.7 + - - -
132I ASP 4.5 3.8 - - - -
133I ILE* 3.4 43.6 - - + +
136I LEU* 5.6 5.4 - - + -
166I VAL* 6.3 1.8 - - + -
169I MET* 4.1 22.1 - - + +
239I ILE* 4.4 6.1 - - + -
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Residues in contact with PHE 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I GLY 3.3 26.5 - - - +
124I ALA* 3.6 9.4 - - + +
125I LEU 3.2 0.8 - - - -
126I TYR* 1.3 86.8 - + + +
128I GLY* 1.3 60.7 + - - +
129I SER 4.6 0.2 - - - -
131I GLY* 3.7 35.0 + - - +
291I ARG* 3.4 35.3 + - - -
342I GLU* 5.8 4.0 - - + -
399I GLN* 6.1 0.4 - - - -
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Residues in contact with GLY 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I ALA 2.5 23.0 + - - -
125I LEU 3.4 2.5 - - - -
127I PHE* 1.3 77.2 - - - +
129I SER* 1.3 60.1 + - - +
238I LEU* 5.2 1.3 - - - +
288I THR* 5.9 0.9 - - - +
291I ARG* 4.0 37.6 - - - +
292I ILE* 4.7 1.9 + - - +
295I ARG* 4.6 17.5 - - - +
342I GLU* 4.9 5.6 - - - -
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Residues in contact with SER 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I LEU 2.7 18.3 + - - -
126I TYR* 2.9 10.6 + - - -
127I PHE 4.6 0.4 - - - -
128I GLY* 1.3 77.7 - - - +
130I ILE* 1.3 73.1 + - - +
235I GLN* 3.5 27.7 + - - +
238I LEU* 3.9 17.0 - - - +
239I ILE* 3.7 15.6 - - - +
288I THR* 4.6 4.6 - - - +
292I ILE* 3.8 22.3 - - - +
295I ARG* 5.9 1.3 - - - +
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Residues in contact with ILE 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I TYR* 2.4 41.4 + - + +
127I PHE 4.6 0.4 - - - -
129I SER* 1.3 84.1 - - - +
131I GLY* 1.3 57.4 + - - +
132I ASP 3.7 19.0 + - - +
136I LEU* 4.2 29.6 - - + -
162I LEU* 5.1 18.8 - - + -
166I VAL* 5.4 2.9 - - + -
235I GLN* 3.3 32.8 - - + +
239I ILE* 5.9 2.2 - - + -
288I THR* 5.1 10.3 - - - +
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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