Contacts of the helix formed by residues 111 - 118 (chain A) in PDB entry 4O91
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLY* 1.3 74.3 - - - -
112A LEU* 1.3 64.9 + - - +
113A TYR* 3.3 11.8 + - - +
114A ASN* 3.0 35.2 + - - +
115A VAL* 3.2 13.9 + - - +
159A PRO 3.9 0.9 - - - -
160A PRO* 3.9 21.2 - - - +
162A LEU 3.3 9.2 - - - -
163A LEU* 4.0 9.3 - - - +
164A LEU* 4.8 1.1 - - - -
176A PHE* 5.9 0.4 - - - -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLY 4.0 0.2 + - - -
111A SER* 1.3 68.5 - - - +
113A TYR* 1.3 65.8 + - - +
115A VAL* 3.2 3.0 + - + +
116A LEU* 2.9 35.7 + - + +
133A TRP* 3.8 34.8 - - + -
159A PRO* 3.5 15.2 + - + +
162A LEU* 2.6 45.2 + - + +
164A LEU* 3.9 27.3 - - + +
171A LEU* 4.7 8.3 - - + -
218A ILE* 4.5 4.9 - - + -
222A VAL* 4.1 20.2 - - + -
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Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 3.2 9.1 - - - +
112A LEU* 1.3 76.5 - - - +
114A ASN* 1.3 61.6 + - + +
116A LEU* 4.5 0.4 - - - +
117A HIS* 2.8 66.0 + + + +
118A GLY* 3.4 12.9 + - - -
159A PRO* 3.3 13.7 + - + +
160A PRO* 3.7 36.6 - - + -
195A TRP* 6.1 4.5 - + - -
221A GLU* 5.3 0.9 - - - -
227A LYS* 3.3 26.9 + - + -
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Residues in contact with ASN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLY 5.0 3.2 + - - -
110A GLY* 4.9 11.3 - - - -
111A SER* 3.0 26.0 + - - +
113A TYR* 1.3 81.8 - - + +
115A VAL* 1.3 62.4 + - - +
118A GLY* 2.8 41.6 + - - +
119A ALA* 3.7 8.1 + - - +
122A LEU* 3.7 4.7 - - - +
123A PRO* 5.2 0.2 - - - +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLY 4.8 10.1 - - - +
111A SER 3.2 6.3 + - - +
112A LEU* 3.2 9.5 + - + +
114A ASN* 1.3 81.7 - - + +
116A LEU* 1.3 61.1 + - + +
122A LEU* 3.6 1.6 - - - +
123A PRO* 3.5 30.8 - - + +
125A TYR* 4.7 3.1 - - + -
133A TRP* 3.9 30.1 - - + -
164A LEU* 3.5 24.9 - - + -
168A GLY* 5.9 0.9 - - - -
225A ARG* 2.9 26.2 + - - +
298A LEU* 4.0 9.0 - - + -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 2.9 45.0 + - + +
115A VAL* 1.3 78.0 - - - +
117A HIS* 1.3 92.0 + - + +
122A LEU* 3.9 8.9 - - - +
125A TYR* 3.4 35.7 - - + +
133A TRP* 4.3 6.5 - - + -
159A PRO* 4.3 7.2 - - + -
221A GLU* 4.0 22.4 - - + +
222A VAL* 4.1 16.4 - - + -
225A ARG* 3.1 27.1 + - + +
468A HIS* 5.6 0.2 + - - -
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Residues in contact with HIS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 2.8 43.0 + + + +
116A LEU* 1.3 96.2 + - + +
118A GLY* 1.3 70.9 + - - +
122A LEU* 4.1 6.2 - - - +
221A GLU* 2.8 28.6 + - + -
225A ARG 3.8 16.2 + - - -
226A ARG 3.7 28.5 - - - -
227A LYS* 3.8 33.0 + - + +
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Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 3.4 11.1 + - - -
114A ASN* 2.8 31.2 + - - -
117A HIS* 1.3 87.8 - - - +
119A ALA* 1.3 64.2 + - - -
120A GLU 3.9 0.9 + - - -
122A LEU* 3.5 14.2 - - - +
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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