Contacts of the helix formed by residues 114 - 124 (chain C) in PDB entry 2NMP
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 TYR 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C LEU* 4.3 3.6 - - + -
113C VAL* 1.3 71.8 - - - +
115C GLY* 1.3 72.8 + - - +
116C GLY* 3.2 32.0 - - - -
117C THR* 2.8 23.1 + - - +
118C ASN 3.1 8.7 + - - -
119C ARG* 5.1 0.3 + - - -
157C GLU* 3.1 14.7 + - - +
161C ASN* 3.8 16.8 + - - +
212C LYS* 4.9 0.4 - - - -
355C THR* 4.2 21.8 - - - -
356C HIS* 3.9 7.4 - + - -
500C PLP 3.4 74.0 + + + +
60D TYR* 4.6 6.2 - - - -
62D ARG* 3.3 27.4 + - - -
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Residues in contact with GLY 115 (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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113C VAL 3.1 3.0 + - - -
114C TYR* 1.3 76.8 - - - +
116C GLY* 1.3 62.3 + - - +
118C ASN* 3.3 4.3 + - - +
119C ARG* 3.0 22.3 + - - +
355C THR 3.9 17.7 - - - -
356C HIS* 3.4 9.3 + - - -
358C SER* 3.8 14.4 + - - -
359C VAL* 4.0 17.7 - - - +
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Residues in contact with GLY 116 (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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91C LEU* 3.6 13.8 - - - +
114C TYR* 3.2 25.6 - - - -
115C GLY* 1.3 74.4 - - - +
117C THR* 1.3 55.2 + - - +
119C ARG* 3.6 28.7 + - - +
120C TYR* 3.1 27.7 + - - +
355C THR 5.0 0.4 + - - -
358C SER* 4.4 0.8 + - - -
242D SER 4.7 0.3 - - - +
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Residues in contact with THR 117 (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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91C LEU* 4.4 7.8 - - - +
94C THR* 4.6 10.3 + - + -
113C VAL* 3.8 15.0 - - + -
114C TYR* 2.8 33.6 + - - +
116C GLY* 1.3 68.4 - - - +
118C ASN* 1.3 70.6 + - - +
120C TYR* 3.1 6.1 + - - +
121C PHE* 3.0 49.0 + - + +
155C TRP* 4.1 20.9 + - + +
157C GLU* 4.4 3.5 + - - -
187C ASP* 4.9 0.9 + - - -
500C PLP 4.5 6.8 - - - -
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Residues in contact with ASN 118 (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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111C ASP 4.6 9.7 + - - -
113C VAL* 3.5 13.7 + - + +
114C TYR 3.1 6.6 + - - +
115C GLY 3.4 9.2 - - - +
117C THR* 1.3 77.6 - - - +
119C ARG* 1.3 59.2 + - - +
121C PHE* 3.7 1.6 - - - +
122C ARG* 2.8 53.0 + - - +
134C PHE* 3.9 28.6 - - - -
358C SER 4.5 0.9 - - - +
359C VAL* 3.9 38.9 - - + +
363C ASP* 4.7 10.0 + - - +
367C LEU* 5.5 1.2 - - - +
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Residues in contact with ARG 119 (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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91C LEU* 4.0 3.8 - - - +
114C TYR* 5.1 0.4 + - - -
115C GLY 3.0 15.0 + - - +
116C GLY* 3.6 21.0 + - - +
118C ASN* 1.3 77.8 + - - +
120C TYR* 1.3 57.9 - - - +
122C ARG* 4.8 2.0 - - - +
123C GLN* 2.9 50.4 + - - +
124C VAL* 4.0 0.5 + - - +
358C SER* 3.6 38.5 + - - +
62D ARG* 3.3 28.3 - - - +
238D PHE* 4.0 19.7 - - + -
241D ASN* 3.4 27.1 + - - +
242D SER* 3.3 25.5 + - - +
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Residues in contact with TYR 120 (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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91C LEU* 5.1 2.9 - - + -
94C THR* 4.1 11.7 - - + -
95C VAL* 3.6 40.8 + - + +
98C THR* 3.0 42.8 + - + +
99C HIS* 4.4 6.8 + - - -
116C GLY 3.1 14.6 + - - +
117C THR* 3.1 6.7 + - - +
119C ARG* 1.3 80.1 - - - +
121C PHE* 1.3 79.8 + + - +
124C VAL* 3.1 38.9 + - + +
125C ALA* 3.0 36.6 + - + +
99D HIS* 4.7 3.6 + - - -
242D SER* 4.2 12.6 - - - +
243D LEU* 3.8 10.1 - - + -
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Residues in contact with PHE 121 (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 THR* 4.0 15.5 - - + -
98C THR* 3.8 28.9 - - + -
107C ILE* 4.2 22.7 - - + -
109C CYS* 3.9 22.4 - - + -
117C THR* 3.0 37.1 + - + -
118C ASN 3.9 4.5 - - - +
120C TYR* 1.3 88.5 - + - +
122C ARG* 1.3 63.4 + - - +
125C ALA* 4.3 9.0 - - + -
126C SER 3.4 12.0 + - - -
132C ILE* 3.2 37.0 - - + +
134C PHE* 4.4 3.4 - + + -
153C LEU* 4.5 1.8 - - + -
155C TRP* 4.0 29.4 - + + -
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Residues in contact with ARG 122 (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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118C ASN* 2.8 33.2 + - - +
119C ARG* 4.2 1.5 - - - +
121C PHE* 1.3 79.5 - - - +
123C GLN* 1.3 94.5 + - - +
126C SER* 2.9 19.5 + - - -
132C ILE* 4.8 4.3 - - - -
134C PHE* 4.5 17.2 - - + -
358C SER 4.3 8.1 + - - -
360C LEU* 3.3 47.4 - - - +
363C ASP* 4.4 14.6 + - - -
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Residues in contact with GLN 123 (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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119C ARG* 2.9 31.7 + - - +
122C ARG* 1.3 112.7 + - - +
124C VAL* 1.3 67.9 + - + +
126C SER* 4.2 4.0 - - - -
127C GLU* 3.7 16.0 - - - +
358C SER* 4.5 3.5 - - - +
238D PHE* 3.5 30.7 - - + -
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Residues in contact with VAL 124 (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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119C ARG 4.4 3.6 - - - +
120C TYR* 3.1 38.2 + - + +
122C ARG 3.7 0.8 - - - -
123C GLN* 1.3 87.5 - - + +
125C ALA* 1.3 68.1 + - - +
126C SER 3.2 1.3 - - - -
127C GLU* 3.0 23.5 + - - +
128C PHE* 3.2 12.9 - - + -
99D HIS* 3.7 24.2 - - + +
238D PHE* 4.1 24.7 - - + -
239D LEU* 4.3 14.8 - - + -
242D SER* 4.6 7.0 - - - -
243D LEU* 3.8 6.1 - - + -
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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