Contacts of the helix formed by residues 120 - 127 (chain D) in PDB entry 2NYM
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D PRO* 5.3 2.1 + - - +
118D GLU 3.8 1.4 + - - -
119D HIS* 1.3 74.0 - - - +
121D PRO* 1.3 64.3 - - - +
122D SER* 3.5 11.7 + - - -
123D ASP* 2.5 58.5 + - - +
124D LEU* 2.9 6.9 + - - -
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Residues in contact with PRO 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D HIS 3.8 4.6 - - - +
120D SER* 1.3 82.7 - - - +
122D SER* 1.3 65.8 + - - +
124D LEU* 3.5 12.9 - - + +
125D GLU* 3.1 33.7 + - - +
157D ARG* 3.6 41.0 - - + +
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Residues in contact with SER 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D SER* 2.6 14.6 + - - -
121D PRO* 1.3 80.5 - - - +
123D ASP* 1.3 63.7 + - - +
125D GLU* 3.9 5.8 + - - +
126D ALA* 3.5 19.1 + - - +
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Residues in contact with ASP 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PRO 4.0 14.9 - - - +
84D GLU* 4.5 3.6 - - - +
86D VAL* 5.6 0.3 - - - +
87D HIS* 3.3 32.1 - - + -
119D HIS* 4.2 12.9 - - + +
120D SER* 2.5 39.3 + - - +
122D SER* 1.3 73.5 - - - +
124D LEU* 1.3 68.8 + - - +
126D ALA* 2.6 17.0 + - - +
127D HIS* 2.7 21.4 + - - +
128D PHE 4.7 1.8 - - - -
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D SER* 4.6 5.6 - - - +
119D HIS* 3.9 20.5 - - + +
120D SER 2.9 7.4 + - - +
121D PRO* 3.5 11.2 - - + +
123D ASP* 1.3 80.5 - - - +
125D GLU* 1.3 56.0 + - - +
126D ALA 2.8 7.8 + - - -
128D PHE* 3.2 47.2 + - + -
129D VAL* 3.1 24.8 + - - -
153D VAL 4.6 0.4 - - - +
154D CYS* 3.9 31.4 - - + +
157D ARG* 3.8 36.1 - - + +
158D VAL* 4.4 7.2 - - + -
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PRO* 3.1 18.9 + - - +
122D SER* 4.1 5.3 - - - +
124D LEU* 1.3 78.6 - - - +
126D ALA* 1.3 56.7 + - + +
129D VAL* 4.5 12.0 - - - +
130D PRO* 3.9 12.0 - - - +
157D ARG 4.4 2.9 - - - +
158D VAL* 3.8 26.2 - - + +
159D SER* 3.3 37.0 + - - +
162D VAL* 4.3 13.5 - - + +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D SER 3.5 15.5 - - - +
123D ASP* 2.6 15.8 + - - +
125D GLU* 1.3 75.3 - - + +
127D HIS* 1.3 78.5 + - + +
130D PRO* 3.8 13.1 - - - +
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Residues in contact with HIS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D HIS* 3.2 54.8 + + + +
90D LEU* 3.8 20.1 - - + +
119D HIS* 5.4 0.4 - - - +
123D ASP* 2.7 21.2 + - - +
126D ALA* 1.3 108.1 - - + +
128D PHE* 1.3 64.6 + - - +
130D PRO* 3.6 6.6 - - - +
131D LEU* 3.5 13.7 + - - +
134D ARG* 4.6 4.0 + - - -
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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