Contacts of the helix formed by residues 114 - 124 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C TYR* 5.0 3.5 - - - -
62C ARG* 3.6 25.3 + - - -
91D LEU* 4.8 5.8 - - + -
113D VAL* 1.3 74.3 - - - +
115D GLY* 1.3 61.9 + - - +
116D GLY* 3.4 23.1 + - - -
117D THR* 2.8 40.1 + - + -
118D ASN 3.1 9.4 + - - -
157D GLU* 2.8 25.9 + - - +
161D ASN* 3.7 21.3 - - - +
212D LYS* 4.8 1.6 - - - -
355D THR* 5.0 17.5 - - + -
356D HIS* 4.1 7.9 - + - -
500D PLP 3.5 55.7 - + + +
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Residues in contact with GLY 115 (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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113D VAL 3.3 3.5 + - - -
114D TYR* 1.3 75.7 - - - +
116D GLY* 1.3 56.3 + - - +
118D ASN* 3.1 10.4 - - - +
119D ARG* 3.0 24.1 + - - +
355D THR 4.7 8.3 - - - -
356D HIS* 3.6 21.0 + - - -
358D SER* 3.5 25.3 + - - -
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Residues in contact with GLY 116 (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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91D LEU* 3.8 11.6 - - - +
114D TYR* 3.3 23.7 - - - -
115D GLY* 1.3 73.1 - - - +
117D THR* 1.3 64.3 + - - +
119D ARG* 3.3 27.3 + - - +
120D TYR* 3.1 24.3 + - - +
355D THR 5.5 0.4 + - - -
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Residues in contact with THR 117 (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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91D LEU* 4.2 6.2 - - + +
94D THR* 4.8 15.5 - - - +
113D VAL* 3.5 10.0 - - + +
114D TYR* 2.8 30.4 + - + +
116D GLY* 1.3 71.3 - - - +
118D ASN* 1.3 64.1 + - - +
120D TYR* 3.3 3.0 + - - +
121D PHE* 3.1 47.9 + - - +
155D TRP* 3.9 14.0 + - + +
157D GLU* 3.6 23.3 - - - +
187D ASP* 4.9 0.7 - - - +
500D PLP 4.7 8.3 - - + +
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Residues in contact with ASN 118 (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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111D ASP 4.5 12.3 + - - -
113D VAL* 3.4 16.7 + - + +
114D TYR 3.1 10.4 + - - +
115D GLY* 3.1 15.5 - - - +
117D THR* 1.3 77.1 + - - +
119D ARG* 1.3 57.0 + - - +
121D PHE* 3.8 1.9 - - - +
122D ARG* 2.9 45.6 + - - +
134D PHE* 3.9 26.9 - - - -
358D SER* 5.4 9.6 + - - +
363D ASP* 5.7 6.5 + - - +
367D LEU* 5.8 2.8 - - - +
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Residues in contact with ARG 119 (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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62C ARG* 4.0 5.7 - - - +
238C PHE* 3.9 28.2 - - + -
241C ASN* 3.4 29.8 + - - -
242C SER* 3.6 16.5 + - - +
91D LEU* 3.9 19.0 - - - +
115D GLY 3.0 15.7 + - - +
116D GLY* 3.7 24.3 + - - +
117D THR 3.3 0.2 - - - -
118D ASN* 1.3 76.1 - - - +
120D TYR* 1.3 57.7 + - - +
122D ARG* 4.5 7.9 - - - +
123D GLN* 2.7 54.9 + - - +
124D VAL* 3.7 0.3 + - - +
358D SER* 4.6 22.5 + - - -
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Residues in contact with TYR 120 (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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99C HIS* 4.9 4.0 + - - -
242C SER* 4.1 15.9 - - - +
243C LEU* 3.9 21.5 - - + -
91D LEU* 4.7 4.3 - - + -
94D THR* 3.9 13.9 - - + -
95D VAL* 3.8 33.5 + - + +
98D THR* 2.7 44.4 + - + -
99D HIS* 4.3 6.4 + - - -
116D GLY 3.1 15.8 + - - +
117D THR* 4.0 2.0 - - - +
119D ARG* 1.3 77.8 - - - +
121D PHE* 1.3 68.3 + + - +
124D VAL* 2.9 40.1 + - + -
125D ALA* 2.7 45.4 + - + +
130D LEU* 5.6 0.3 - - - +
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Residues in contact with PHE 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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94D THR* 4.1 7.4 - - + -
98D THR* 3.5 28.5 - - + -
107D ILE* 3.9 26.7 - - + -
109D CYS* 3.6 33.2 - - + -
117D THR* 3.1 33.1 + - - +
118D ASN 3.8 3.1 - - - +
120D TYR* 1.3 88.9 - + - +
122D ARG* 1.3 61.5 + - - +
125D ALA* 4.0 8.5 - - + -
126D SER 3.3 12.8 + - - -
132D ILE* 3.1 35.1 - - + +
134D PHE* 4.4 3.4 - - + -
153D LEU* 4.6 1.3 - - + -
155D TRP* 3.8 33.2 - + + -
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Residues in contact with ARG 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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118D ASN* 2.9 33.7 + - - +
119D ARG* 4.1 6.4 - - - +
121D PHE* 1.3 77.5 - - - +
123D GLN* 1.3 88.7 + - - +
126D SER* 2.7 27.7 + - - -
132D ILE* 4.9 4.0 - - - -
134D PHE* 4.4 17.5 - - + -
358D SER* 4.8 17.0 - - - -
363D ASP* 5.3 8.1 - - - -
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Residues in contact with GLN 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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238C PHE* 3.6 27.3 - - + -
119D ARG* 2.7 36.1 + - + +
122D ARG* 1.3 110.3 + - + +
124D VAL* 1.3 64.7 + - + +
126D SER* 4.5 2.9 - - - -
127D GLU* 3.8 15.6 - - - +
358D SER* 5.7 1.0 - - - -
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Residues in contact with VAL 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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99C HIS* 3.6 32.5 - - + +
238C PHE* 4.1 17.3 - - + -
239C LEU* 4.1 22.2 - - + -
242C SER* 4.4 6.3 - - - -
243C LEU* 4.0 6.1 - - + -
119D ARG 4.6 0.9 - - - +
120D TYR* 2.9 37.3 + - + +
123D GLN* 1.3 83.1 - - - +
125D ALA* 1.3 66.8 + - - +
126D SER 3.2 1.3 - - - -
127D GLU* 3.1 15.5 + - - +
128D PHE* 3.4 15.9 - - + -
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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