Contacts of the helix formed by residues 120 - 126 (chain E) in PDB entry 6ACQ
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 SER 120 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A ARG* 3.7 25.2 - - - -
92E MET* 3.8 4.9 - - - +
119E LEU* 1.3 72.2 - - - +
121E ILE* 1.3 62.6 + - - +
122E THR* 3.3 4.2 + - - -
123E GLU* 2.8 34.6 + - - +
124E VAL* 3.1 25.3 + - - +
181E GLU* 2.9 25.5 + - - -
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Residues in contact with ILE 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E SER* 4.0 19.5 - - - +
116E THR* 4.1 17.0 - - + -
119E LEU 3.4 3.0 + - - +
120E SER* 1.3 72.2 - - - +
122E THR* 1.3 63.1 + - - +
124E VAL* 3.3 9.5 + - + +
125E ALA* 3.0 22.5 + - + +
134E VAL* 4.4 7.2 - - + +
135E ILE* 3.5 30.3 - - - +
136E GLY* 3.4 31.0 - - - +
152E ILE* 4.2 15.5 - - + +
154E GLY* 4.0 18.6 - - - +
181E GLU* 3.2 12.0 + - + +
185E PHE* 5.5 2.7 - - + -
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Residues in contact with THR 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LYS* 3.4 33.5 - - + +
265A ARG* 3.9 2.0 - - + -
266A ALA* 3.6 23.1 - - + +
120E SER* 3.5 4.0 - - - -
121E ILE* 1.3 74.8 - - - +
123E GLU* 1.3 61.2 + - - +
125E ALA* 3.4 8.2 + - - +
126E SER* 3.3 20.3 + - - -
154E GLY* 3.6 4.4 - - - -
155E ILE* 3.3 27.3 + - + +
156E ALA* 5.5 1.8 - - + +
181E GLU* 2.5 31.6 + - - -
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Residues in contact with GLU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ARG* 3.4 49.5 + - + +
92E MET* 3.5 27.7 - - + +
96E LYS* 3.2 31.7 + - - +
120E SER* 2.8 23.3 + - - +
122E THR* 1.3 70.4 - - - +
124E VAL* 1.3 67.5 + - - +
126E SER* 3.3 15.8 + - - -
127E ALA 3.9 2.3 + - - -
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Residues in contact with VAL 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E MET* 3.7 23.3 - - + -
95E LYS* 4.2 24.0 - - + +
96E LYS* 4.7 5.2 - - + +
99E PHE* 3.4 50.0 - - + -
114E SER* 5.8 2.9 - - - +
116E THR* 6.0 1.8 - - + -
119E LEU* 5.2 2.2 - - + -
120E SER 3.1 16.6 + - - +
121E ILE* 3.7 11.7 - - + +
123E GLU* 1.3 76.2 - - - +
125E ALA* 1.3 59.0 + - - +
127E ALA* 2.9 28.2 + - - +
128E THR* 4.0 3.3 + - - +
134E VAL* 4.7 1.8 - - + -
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Residues in contact with ALA 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ILE* 3.0 17.7 + - + +
122E THR* 3.6 8.7 - - - +
123E GLU 3.3 0.2 - - - -
124E VAL* 1.3 76.6 - - - +
126E SER* 1.3 57.6 + - - +
128E THR* 3.1 28.8 + - - +
131E PRO* 3.7 24.8 - - + +
134E VAL* 3.5 35.7 - - + +
154E GLY* 6.4 0.9 - - - -
156E ALA* 5.7 2.2 - - + -
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Residues in contact with SER 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ARG 2.7 25.2 + - - -
266A ALA* 3.2 22.3 + - - -
267A GLY* 4.8 1.1 - - - -
96E LYS* 6.3 0.4 - - - -
122E THR 3.3 4.5 + - - -
123E GLU* 3.3 13.2 + - - -
124E VAL 3.1 0.8 + - - -
125E ALA* 1.3 74.4 - - - +
127E ALA* 1.3 60.9 + - - +
128E THR 3.2 7.3 + - - +
131E PRO* 5.4 2.0 - - - -
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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