Contacts of the helix formed by residues 140 - 152 (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 ALA 140 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328E PRO* 4.5 11.9 - - + -
130F TYR* 4.0 30.3 - - + +
134F LEU* 4.1 4.5 - - + -
139F ASN* 1.3 76.5 - - - +
141F ASN* 1.3 66.7 + - - +
142F VAL 3.4 2.0 - - - -
143F TRP* 3.2 14.3 + - + +
144F LYS* 2.9 21.9 + - + +
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Residues in contact with ASN 141 (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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25F GLU* 3.0 34.6 + - - +
139F ASN* 2.8 21.4 + - - +
140F ALA* 1.3 75.0 + - - +
142F VAL* 1.3 65.7 + - - +
144F LYS* 3.0 8.2 + - - +
145F TYR* 2.8 52.6 + - + -
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Residues in contact with VAL 142 (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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25F GLU* 4.0 18.2 - - + +
28F VAL* 4.0 8.3 - - + -
94F VAL* 5.3 0.9 - - + -
133F CYS* 4.1 12.6 - - + -
137F TYR* 3.3 61.2 - - + +
139F ASN* 4.0 1.8 + - - +
140F ALA 3.4 0.4 - - - -
141F ASN* 1.3 75.4 - - - +
143F TRP* 1.3 64.6 + - - +
145F TYR* 3.4 9.2 + - - +
146F PHE* 3.0 50.1 + - + -
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Residues in contact with TRP 143 (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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328E PRO* 5.2 7.6 - - + -
372E TRP* 4.3 10.8 - + - -
121F ARG* 3.7 34.8 - - + -
124F THR* 2.8 22.2 + - - -
125F GLN* 3.2 28.9 - - + -
129F PHE* 3.7 18.4 - + - -
130F TYR* 3.5 46.9 - + + +
133F CYS* 4.1 20.7 - - + +
140F ALA* 3.2 17.3 + - + +
141F ASN 3.1 0.4 - - - -
142F VAL* 1.3 80.3 - - - +
144F LYS* 1.3 88.4 + - + +
146F PHE* 3.2 1.2 + - - +
147F THR* 2.9 48.8 + - + +
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Residues in contact with LYS 144 (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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140F ALA* 2.9 13.1 + - + +
141F ASN* 3.5 12.3 - - - +
143F TRP* 1.3 87.4 - - + +
145F TYR* 1.3 79.1 - - + +
146F PHE 2.9 0.2 + - - -
147F THR* 2.7 21.8 + - - -
148F ASP* 2.9 40.4 + - - +
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Residues in contact with TYR 145 (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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25F GLU* 3.8 24.5 + - + -
28F VAL* 4.6 2.9 - - + -
29F LYS* 3.2 68.6 + - + +
32F CYS* 3.7 28.0 - - + +
36F LYS* 5.1 1.9 - - - -
141F ASN* 2.8 50.4 + - + +
142F VAL* 3.7 9.0 - - - +
144F LYS* 1.3 90.0 - - + +
146F PHE* 1.3 58.8 + - - +
148F ASP* 3.7 8.1 - - - +
149F LEU 3.5 12.8 + - - -
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Residues in contact with PHE 146 (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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28F VAL* 3.4 26.2 - - + -
31F LEU* 5.3 2.2 - - + -
32F CYS* 3.9 16.2 - - - -
94F VAL* 5.2 3.1 - - + -
97F VAL* 4.0 30.5 - - + -
98F THR* 3.4 35.2 - - + -
101F VAL* 4.5 9.9 - - + -
129F PHE* 3.9 25.6 - + + -
142F VAL* 3.0 37.6 + - + +
143F TRP 3.7 2.7 - - - +
145F TYR* 1.3 72.9 - - - +
147F THR* 1.3 68.1 + - - +
148F ASP 3.0 1.6 - - - -
149F LEU* 2.9 18.1 + - + +
150F PHE* 2.9 25.9 + + + -
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Residues in contact with THR 147 (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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115F ARG* 5.1 0.5 + - - -
121F ARG* 3.6 35.1 + - + +
124F THR* 4.2 5.8 - - + +
129F PHE* 4.9 1.6 - - + -
143F TRP* 2.9 57.4 + - + +
144F LYS* 2.7 24.4 + - - -
146F PHE* 1.3 75.0 - - - +
148F ASP* 1.3 65.9 + - - +
150F PHE* 3.3 35.3 - - + +
151F ASP* 3.7 4.3 + - - +
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Residues in contact with ASP 148 (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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36F LYS* 4.3 19.5 + - - +
121F ARG* 3.4 20.4 + - - +
144F LYS* 2.9 53.6 + - - +
145F TYR* 3.7 9.4 - - - +
147F THR* 1.3 80.4 + - - +
149F LEU* 1.3 62.7 + - - +
151F ASP* 3.4 20.6 + - - +
152F TYR* 3.5 11.7 - - + -
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Residues in contact with LEU 149 (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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32F CYS* 3.5 24.9 - - + +
35F ALA* 3.3 36.6 - - + -
36F LYS* 3.5 20.2 - - + +
39F LEU* 3.8 16.1 - - + +
101F VAL* 3.8 31.4 - - + -
145F TYR 3.5 10.3 + - - +
146F PHE* 2.9 14.9 + - + +
148F ASP* 1.3 79.0 - - - +
150F PHE* 1.3 68.9 + - + +
152F TYR* 2.9 24.0 + - - +
153F LEU* 3.8 5.9 + - + +
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Residues in contact with PHE 150 (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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86F TYR* 5.4 2.0 - + - -
87F VAL* 4.2 21.5 - - + -
97F VAL* 4.2 18.4 - - + -
101F VAL* 5.9 1.1 - - + -
115F ARG* 3.5 7.8 - - - +
118F HIS 4.4 0.7 - - - -
119F GLU* 3.2 64.4 - - + +
120F SER* 4.0 0.9 - - - -
124F THR* 4.4 15.7 - - + -
129F PHE* 4.4 3.8 - + - -
146F PHE* 2.9 36.9 + + + -
147F THR* 3.3 26.5 - - + +
149F LEU* 1.3 80.1 - - + +
151F ASP* 1.3 53.8 + - - +
153F LEU* 2.6 46.0 + - + +
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Residues in contact with ASP 151 (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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115F ARG* 2.9 36.4 + - - +
121F ARG* 2.7 33.9 + - - -
147F THR 4.0 0.4 - - - -
148F ASP* 3.4 13.6 + - - +
149F LEU 3.2 0.4 - - - -
150F PHE* 1.3 77.2 - - - +
152F TYR* 1.3 65.3 - - + +
153F LEU 3.2 8.3 + - - +
185F ARG 3.6 11.1 - - - +
186F LEU* 3.8 10.8 - - - +
187F GLN* 3.2 31.3 - - - +
188F GLU 3.3 3.2 + - - -
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Residues in contact with TYR 152 (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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36F LYS* 3.8 42.7 + - + +
39F LEU* 3.4 28.7 - - + +
40F THR* 3.6 29.4 - - + -
148F ASP* 3.5 20.0 - - + -
149F LEU 2.9 10.9 + - - +
151F ASP* 1.3 81.4 - - + +
153F LEU* 1.3 61.8 + - - +
154F PRO* 3.5 0.9 - - - +
185F ARG* 3.2 16.9 + - - +
186F LEU* 3.9 31.4 - - + -
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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