Contacts of the strand formed by residues 141 - 149 (chain F) in PDB entry 3N2N
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 THR 141 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40F TYR* 4.0 7.4 - - - -
42F GLY* 3.3 24.9 - - - +
44F ASP* 3.4 28.1 + - - +
79F ARG* 5.8 0.7 + - - -
134F GLU* 6.0 2.0 - - - +
135F ASN* 6.1 0.7 - - - -
139F TYR* 3.3 21.3 + - - +
140F ARG* 1.3 78.7 + - - +
142F ALA* 1.3 73.7 + - - +
143F SER* 3.2 17.2 + - - +
172F GLY 5.1 3.3 - - - +
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Residues in contact with ALA 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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40F TYR* 3.5 27.6 - - + -
42F GLY 3.0 10.2 + - - +
43F PHE* 3.5 6.2 - - + -
44F ASP 2.9 27.4 + - - +
141F THR* 1.3 70.6 - - - +
143F SER* 1.3 59.3 + - - +
144F VAL* 3.8 8.5 - - + -
174F ILE* 5.8 6.7 - - + -
215F ILE* 3.6 32.3 - - + -
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Residues in contact with SER 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ASP* 3.5 11.0 + - - +
46F TYR* 4.4 13.7 + - - -
131F ILE* 4.4 15.4 - - - +
134F GLU* 6.0 1.0 - - - +
135F ASN* 5.1 3.3 + - - -
141F THR* 3.2 22.8 + - - +
142F ALA* 1.3 69.6 - - - +
144F VAL* 1.3 62.3 + - - +
172F GLY 4.0 16.1 + - - +
173F ALA* 3.3 12.8 - - - -
174F ILE* 2.9 28.0 + - - +
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Residues in contact with VAL 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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43F PHE* 3.8 22.4 - - + -
44F ASP 2.8 11.2 + - - +
45F LEU* 3.4 24.6 - - + +
46F TYR* 2.7 34.0 + - - -
142F ALA* 4.2 7.9 - - + +
143F SER* 1.3 76.9 - - - +
145F ILE* 1.3 60.6 + - - +
146F ILE* 4.4 2.9 - - + -
174F ILE* 3.5 15.5 - - + +
176F TYR* 3.7 32.1 - - + -
208F LEU* 5.6 1.3 - - + -
211F ILE* 5.8 1.1 - - + -
212F ILE* 6.3 1.6 - - + -
215F ILE* 4.0 18.2 - - + -
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Residues in contact with ILE 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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46F TYR* 3.4 22.7 - - + +
48F ILE* 3.6 23.6 - - + -
124F PHE* 3.8 22.2 - - + -
127F ALA* 4.1 14.1 - - + -
131F ILE* 4.1 3.4 - - + -
144F VAL* 1.3 75.3 - - - +
146F ILE* 1.3 65.4 + - - +
147F ALA 4.2 1.6 - - - +
168F SER* 3.7 33.4 - - - +
173F ALA* 3.9 14.6 - - + -
174F ILE 2.8 14.0 + - - +
175F VAL* 4.1 10.8 - - + -
176F TYR* 2.7 35.2 + - - +
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Residues in contact with ILE 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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45F LEU* 3.7 27.8 - - + -
46F TYR 2.9 9.7 + - - +
47F PHE* 3.5 26.0 - - + -
48F ILE 2.9 25.0 + - - +
65F PHE* 4.0 5.8 - - + -
69F LEU* 4.2 9.2 - - + -
144F VAL* 4.4 4.0 - - + -
145F ILE* 1.3 77.4 - - - +
147F ALA* 1.3 61.4 + - - +
148F LEU* 3.5 26.6 + - + +
176F TYR* 3.5 7.6 - - + +
178F VAL* 3.8 19.3 - - + -
208F LEU* 3.9 31.2 - - + -
212F ILE* 4.6 2.9 - - + -
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Residues in contact with ALA 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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48F ILE* 3.3 14.8 - - + +
85F PHE* 5.9 0.2 - - + -
120F MET* 4.7 11.0 - - - -
124F PHE* 4.0 30.7 - - + -
145F ILE* 4.0 1.3 - - + -
146F ILE* 1.3 71.8 - - - +
148F LEU* 1.3 58.4 + - - +
149F THR* 3.9 3.9 + - + +
176F TYR 2.8 16.1 + - - +
177F ALA* 3.3 9.0 - - + +
178F VAL 2.8 31.7 + - - +
191F ILE* 5.2 1.8 - - + -
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Residues in contact with LEU 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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47F PHE* 4.9 1.3 - - + -
48F ILE 2.9 9.0 + - - +
49F LEU* 3.8 24.9 - - + -
50F ASP* 2.9 30.7 + - - +
62F ILE* 3.9 23.3 - - + +
65F PHE* 3.7 30.1 - - + -
85F PHE* 4.4 1.0 - - - -
146F ILE* 3.5 33.7 - - + +
147F ALA* 1.3 71.4 - - - +
149F THR* 1.3 61.8 + - - +
178F VAL* 3.5 31.2 - - + +
180F VAL* 4.6 5.8 - - + -
201F VAL* 4.1 14.8 - - + -
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Residues in contact with THR 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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50F ASP* 2.6 29.1 + - - -
55F VAL* 5.4 0.7 - - - -
62F ILE* 5.7 0.2 - - - -
85F PHE* 4.3 1.4 - - - -
120F MET* 4.0 24.7 - - + -
147F ALA* 4.7 7.9 - - + +
148F LEU* 1.3 76.2 - - - +
150F ASP* 1.3 64.4 + - - +
151F GLY* 3.1 16.7 + - - +
153F LEU* 4.2 7.1 - - - +
177F ALA* 5.6 1.3 - - + -
178F VAL 3.3 4.8 + - - +
179F GLY* 3.4 8.3 - - - -
180F VAL* 2.9 28.6 + - - +
188F LEU* 3.8 23.6 - - + +
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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