Contacts of the helix formed by residues 137 - 142 (chain A) in PDB entry 2D2O
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 PHE 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLN* 4.1 3.0 + - - +
136A ILE* 1.3 72.8 - - - +
138A PRO* 1.3 59.8 - - - +
139A GLU* 3.3 3.1 - - + -
140A ARG* 2.9 49.5 + - + -
141A PHE* 3.2 9.2 + - - +
193A THR* 3.4 26.5 - - + -
201A HIS* 3.8 20.2 - + - -
202A HIS* 3.9 24.5 - - + -
204A TYR* 5.3 0.4 - + - -
420A HIS* 3.9 30.3 - + + -
453A TYR* 4.9 4.0 - - + +
454A TYR* 3.6 26.5 - + + -
469A ARG* 3.5 40.8 - - + -
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Residues in contact with PRO 138 (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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136A ILE* 2.9 34.9 - - + +
137A PHE* 1.3 77.4 - - + +
139A GLU* 1.3 61.3 - - - +
140A ARG 3.0 1.3 + - - -
141A PHE* 3.5 8.0 + - + +
170A GLY* 3.0 20.4 - - - -
171A ASP* 3.4 7.7 + - - +
172A LEU* 4.9 9.6 - - + -
175A VAL* 5.5 2.0 - - + -
192A PHE* 4.7 3.4 - - + -
193A THR* 3.2 16.4 - - - +
194A PRO 4.1 2.9 - - - +
195A ILE* 3.9 17.9 - - + -
216A PHE* 3.7 34.3 - - + -
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Residues in contact with GLU 139 (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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137A PHE* 3.1 5.3 + - + -
138A PRO* 1.3 79.7 - - - +
140A ARG* 1.3 95.2 + - + +
150A PRO* 3.9 5.4 - - - +
167A PHE* 3.4 22.7 - - + +
168A TYR* 2.9 18.3 + - - +
169A GLY* 2.9 28.4 + - - -
170A GLY* 2.9 20.1 + - - +
201A HIS* 3.4 35.4 - - + +
215A GLN* 4.9 4.0 - - - +
216A PHE* 3.7 19.1 - - + -
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Residues in contact with ARG 140 (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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137A PHE* 2.9 23.5 + - + +
139A GLU* 1.3 98.3 + - - +
141A PHE* 1.3 59.0 + - - +
156A TRP* 3.4 9.9 - - - -
162A PRO* 3.7 16.0 - - - +
163A ARG 4.8 1.6 + - - -
166A SER* 2.8 34.4 + - - +
168A TYR* 3.2 28.3 - - - -
201A HIS* 3.0 29.9 + - - +
454A TYR* 3.5 21.8 - - - +
466A PRO* 4.7 0.6 + - - +
469A ARG* 2.6 53.5 + - - +
470A ARG 3.8 3.1 - - - +
471A PRO* 4.1 3.4 - - + -
472A MET* 2.8 29.8 + - - +
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Residues in contact with PHE 141 (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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134A TYR* 3.6 21.5 - - - -
136A ILE* 3.7 44.0 - - + -
137A PHE 3.2 6.8 + - - +
138A PRO* 3.5 6.0 + - + +
140A ARG* 1.3 79.0 - - - +
142A ALA* 1.3 65.9 + - + +
156A TRP* 3.3 2.9 - - - -
175A VAL* 4.0 20.9 - - + -
178A ARG* 3.7 23.1 - - + -
182A LEU* 4.0 24.0 - - + -
454A TYR* 4.1 17.7 - + + -
472A MET* 3.1 15.1 - - + +
474A TRP* 2.9 49.0 + + - -
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Residues in contact with ALA 142 (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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138A PRO 4.4 0.4 + - - -
141A PHE* 1.3 85.8 - - + +
143A ASN* 1.3 60.6 + - - +
144A GLY 3.3 3.7 + - - -
156A TRP* 3.5 5.7 - - - -
170A GLY* 3.8 5.6 - - - -
171A ASP 2.8 30.2 + - - +
174A GLY* 3.4 25.1 - - - -
178A ARG* 3.7 23.6 - - + -
474A TRP* 3.9 8.1 - - + +
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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