Contacts of the helix formed by residues 128 - 138 (chain C) 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 GLY 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C ASP* 3.0 4.8 + - - -
89C ARG 5.4 0.4 - - - -
93C SER* 5.5 0.9 - - - -
124C THR 3.2 6.0 + - - -
125C GLN 4.1 2.5 + - - -
126C VAL 3.5 3.6 + - - -
127C TYR* 1.3 79.2 - - - +
129C PHE* 1.3 65.6 + - - +
130C TYR 2.9 4.2 + - - -
131C ASP* 3.1 13.4 + - - +
132C GLU* 2.9 24.0 + - - +
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Residues in contact with PHE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C VAL* 3.7 37.5 - - + -
88C ASP* 3.3 9.4 + - - +
93C SER* 3.6 22.9 - - - -
94C VAL* 3.9 24.2 - - + -
97C VAL* 4.1 2.2 - - + -
124C THR* 3.2 26.0 + - + -
128C GLY* 1.3 73.8 - - - +
130C TYR* 1.3 63.8 + - - +
132C GLU* 3.7 2.6 + - + +
133C CYS* 3.0 42.7 + - - -
143C TRP* 3.9 17.3 - + - -
146C PHE* 3.7 40.6 - + + -
147C THR* 5.1 0.2 - - + -
150C PHE* 4.3 6.7 - + - -
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Residues in contact with TYR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B SER* 3.4 26.2 - - - -
327B SER* 4.8 0.5 + - - -
328B PRO* 3.5 27.5 - - + +
329B HIS* 3.8 17.9 - + + +
124C THR 3.1 15.6 + - - +
125C GLN* 3.7 25.8 - - + +
128C GLY 2.9 1.4 + - - -
129C PHE* 1.3 72.6 - - - +
131C ASP* 1.3 82.9 + - - +
133C CYS* 2.7 21.1 + - - +
134C LEU* 3.1 38.2 + - + +
140C ALA* 4.4 11.5 - - + +
143C TRP* 3.6 44.8 - + + +
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Residues in contact with ASP 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B THR 4.0 6.9 - - - +
287B HIS* 3.7 13.4 + - - -
288B SER* 3.0 33.6 + - - -
289B PRO* 3.2 27.0 - - - +
125C GLN 5.0 4.7 + - - +
128C GLY* 3.1 12.9 + - - +
130C TYR* 1.3 86.0 - - - +
132C GLU* 1.3 64.9 + - - +
134C LEU* 2.7 19.7 + - - +
135C ARG* 2.8 16.1 + - - +
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Residues in contact with GLU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLY 4.1 4.3 - - - +
91C TYR* 3.4 12.5 - - - +
93C SER* 2.9 30.1 + - - -
94C VAL* 2.9 31.8 + - + +
128C GLY 2.9 19.4 + - - +
129C PHE* 3.9 5.6 - - - +
131C ASP* 1.3 71.8 - - - +
133C CYS* 1.3 65.1 + - - +
135C ARG* 3.4 28.2 + - - +
136C LYS* 2.9 51.9 + - + +
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Residues in contact with CYS 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C VAL* 4.4 12.1 - - - -
129C PHE* 3.0 47.3 + - - +
130C TYR 2.7 19.2 + - - +
132C GLU* 1.3 71.5 - - - +
134C LEU* 1.3 52.1 + - + +
136C LYS 3.6 0.3 - - - -
137C TYR* 2.7 42.3 + - + +
139C ASN* 4.9 1.1 - - - +
140C ALA* 5.8 1.6 - - - -
142C VAL* 4.2 11.2 - - + -
143C TRP* 3.8 36.1 - - + +
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LYS 3.8 20.0 - - - +
286B THR* 4.0 21.4 - - + +
287B HIS 5.0 0.4 - - - +
288B SER* 5.2 0.4 - - - +
130C TYR* 3.1 47.1 + - + +
131C ASP* 2.7 18.4 + - - +
133C CYS* 1.3 68.2 - - + +
135C ARG* 1.3 54.3 + - - +
136C LYS 2.5 17.9 + - - -
138C GLY* 2.8 28.7 + - - +
139C ASN 2.9 31.6 - - - +
140C ALA* 3.8 19.3 - - + -
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Residues in contact with ARG 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B THR* 3.9 25.7 - - - +
91C TYR* 3.3 57.6 + - - -
131C ASP* 2.8 17.7 + - + +
132C GLU* 3.7 27.1 + - - +
134C LEU* 1.3 71.0 - - - +
136C LYS* 1.3 78.0 + - - +
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Residues in contact with LYS 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLN* 3.4 36.7 + - - +
91C TYR* 3.5 15.4 + - - -
92C TYR* 3.8 5.2 - - - +
94C VAL* 4.1 6.1 - - + -
95C GLU* 2.8 38.5 + - - +
132C GLU* 2.9 37.3 + - + +
133C CYS* 4.0 1.8 - - - +
134C LEU 2.5 11.4 + - - -
135C ARG* 1.3 103.6 - - - +
137C TYR* 1.3 64.8 + - + +
138C GLY 3.7 0.4 - - - -
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLN* 3.1 32.6 - - - +
23C LEU 2.5 29.1 + - - -
24C SER* 4.3 1.3 - - - -
25C GLU* 3.7 23.2 - - + +
28C VAL* 3.5 12.9 - - + +
94C VAL* 3.8 22.9 - - + +
98C THR* 4.8 0.2 + - - -
133C CYS* 2.7 26.4 + - - +
136C LYS* 1.3 77.5 - - + +
138C GLY* 1.3 56.7 + - - +
139C ASN* 3.1 25.5 + - - +
142C VAL* 3.2 47.3 - - + -
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Residues in contact with GLY 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B THR* 5.7 3.7 - - - +
134C LEU* 2.8 21.6 + - - +
136C LYS 3.7 0.6 - - - -
137C TYR* 1.3 74.2 - - - +
139C ASN* 1.3 61.4 + - - +
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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