Contacts of the helix formed by residues 128 - 138 (chain F) in PDB entry 2NPP
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88F ASP* 5.1 0.4 - - - -
89F ARG 5.2 1.1 - - - -
124F THR 3.5 3.7 + - - -
125F GLN 4.7 2.0 + - - -
126F VAL 3.7 2.6 + - - -
127F TYR* 1.3 77.0 - - - +
129F PHE* 1.3 66.9 + - - -
130F TYR 3.1 2.9 - - - -
131F ASP* 2.6 29.5 + - - +
132F GLU* 3.2 9.4 + - - -
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Residues in contact with PHE 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F VAL* 3.5 28.3 - - + -
88F ASP* 3.0 25.4 + - - +
93F SER* 3.4 28.3 + - - -
94F VAL* 4.1 12.1 - - + -
97F VAL* 4.1 6.1 - - + -
124F THR* 3.5 20.2 + - + -
127F TYR 3.7 0.4 + - - -
128F GLY* 1.3 67.7 - - - +
130F TYR* 1.3 62.9 + - - +
132F GLU* 3.2 6.6 + - + +
133F CYS* 2.9 51.8 + - - -
143F TRP* 3.7 25.4 - + - -
146F PHE* 3.9 37.7 - + + -
147F THR* 4.9 0.7 - - + -
150F PHE* 4.4 6.7 - + - -
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Residues in contact with TYR 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E SER* 3.7 15.5 - - - -
327E SER* 4.6 1.6 + - - -
328E PRO* 3.5 28.8 - - + +
329E HIS* 3.5 31.0 - - + +
124F THR 3.1 15.0 + - - +
125F GLN* 3.8 21.5 - - + -
128F GLY 2.6 4.2 + - - -
129F PHE* 1.3 76.3 - - - +
131F ASP* 1.3 68.2 + - - +
133F CYS* 3.1 4.5 + - - +
134F LEU* 3.0 45.6 + - + +
140F ALA* 4.0 22.0 - - + +
143F TRP* 3.5 40.0 - + + -
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Residues in contact with ASP 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E THR 4.1 11.9 - - - +
287E HIS* 3.5 8.3 + - - -
288E SER* 2.8 45.7 + - - -
289E PRO* 3.7 7.8 - - - +
125F GLN 4.2 8.7 - - - +
128F GLY* 2.6 21.2 + - - +
130F TYR* 1.3 79.6 - - - +
132F GLU* 1.3 55.9 + - - +
134F LEU* 2.6 31.2 + - - +
135F ARG* 2.9 24.2 + - - +
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Residues in contact with GLU 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F GLY 4.1 3.5 - - - +
91F TYR 3.5 12.3 - - - +
93F SER* 2.9 30.5 + - - -
94F VAL* 2.5 41.2 + - + +
128F GLY 3.2 6.1 + - - +
129F PHE* 3.2 13.7 + - - +
131F ASP* 1.3 77.7 - - - +
133F CYS* 1.3 66.4 + - - +
135F ARG* 3.1 23.5 + - + +
136F LYS* 2.8 57.2 + - + +
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Residues in contact with CYS 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F VAL* 4.0 11.0 - - - -
129F PHE* 2.9 54.6 + - - -
130F TYR 3.4 7.9 - - - +
132F GLU* 1.3 75.5 - - - +
134F LEU* 1.3 63.3 + - - +
137F TYR* 2.9 34.7 + - - +
139F ASN 3.9 4.7 - - - +
142F VAL* 4.1 14.4 - - + -
143F TRP* 4.1 28.3 - - + +
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E LYS 3.2 26.5 - - - +
286E THR* 4.1 15.6 - - + +
287E HIS 5.3 0.4 - - - +
288E SER* 5.3 3.1 - - - +
130F TYR* 3.0 50.5 + - + +
131F ASP* 2.6 19.6 + - - +
133F CYS* 1.3 72.6 - - + +
135F ARG* 1.3 59.1 + - - +
138F GLY* 2.5 38.1 + - - +
139F ASN* 3.1 30.7 - - - +
140F ALA* 4.1 6.1 - - + +
309F LEU* 5.6 0.7 - - + -
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Residues in contact with ARG 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E THR* 3.5 42.5 + - + +
287E HIS* 5.3 7.7 - - - -
91F TYR* 5.6 14.8 - - - -
131F ASP* 2.9 17.9 + - - +
132F GLU* 3.2 37.8 - - - +
134F LEU* 1.3 74.6 - - - +
136F LYS* 1.3 68.5 + - + +
137F TYR 3.8 0.3 + - - -
138F GLY 4.5 0.9 + - - -
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Residues in contact with LYS 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F GLN* 2.9 46.9 + - - +
91F TYR* 3.5 18.6 + - - -
92F TYR* 3.9 4.8 - - - +
94F VAL* 3.9 9.0 - - + -
95F GLU* 2.9 35.1 + - - +
132F GLU* 2.8 48.9 + - + +
135F ARG* 1.3 88.0 - - + +
137F TYR* 1.3 71.9 + - + +
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Residues in contact with TYR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F GLN* 3.5 26.7 - - - +
23F LEU 2.7 30.2 + - - -
24F SER* 4.4 0.7 - - - -
25F GLU* 3.6 24.4 - - + +
28F VAL* 3.6 10.3 - - + +
94F VAL* 3.8 21.9 - - + +
98F THR* 5.2 0.2 + - - -
133F CYS 2.9 19.8 + - - +
136F LYS* 1.3 87.9 - - + +
138F GLY* 1.3 58.1 + - - +
139F ASN* 3.1 28.7 + - - +
142F VAL* 3.3 46.4 - - + +
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Residues in contact with GLY 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F LEU* 2.5 25.7 + - - +
135F ARG 4.5 1.2 + - - -
137F TYR* 1.3 71.1 - - - +
139F ASN* 1.3 57.5 + - - +
309F LEU* 3.4 38.8 - - - +
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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