Contacts of the strand formed by residues 6 - 11 (chain F) in PDB entry 1NUE
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 ARG 6 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3F ASN* 4.7 11.5 + - - -
4F LEU 3.7 6.7 - - - +
5F GLU* 1.3 78.4 - - - +
7F THR* 1.3 59.8 + - - +
34F ARG* 3.2 5.7 - - - +
36F VAL* 3.9 16.3 - - - +
77F VAL* 3.9 14.0 - - + +
78F TRP 3.2 9.0 - - - +
79F GLU* 2.7 44.8 + - - -
83F VAL* 3.9 2.2 - - - -
84F VAL* 3.6 8.1 - - - +
123F VAL* 5.4 1.2 - - - +
126F ALA* 3.5 16.5 - - - +
127F GLU* 4.4 13.4 + - - +
130F ILE* 3.9 12.9 - - + +
139F LEU* 3.7 29.9 - - - +
141F ASP* 3.1 32.1 + - - -
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Residues in contact with THR 7 (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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6F ARG* 1.3 74.6 - - - +
8F PHE* 1.3 67.2 + - - +
9F ILE* 3.9 25.1 + - + +
28F PHE* 5.9 0.2 - - + -
77F VAL* 3.3 7.4 - - - +
78F TRP* 2.9 34.7 + - + +
83F VAL* 3.7 29.8 - - + +
84F VAL* 3.8 22.3 + - - +
87F GLY* 5.6 0.7 - - - -
120F SER* 3.5 23.7 + - - -
126F ALA* 4.0 5.2 - - - -
130F ILE* 4.3 4.9 - - - -
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Residues in contact with PHE 8 (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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7F THR* 1.3 74.8 + - - +
9F ILE* 1.3 64.0 + - - +
10F ALA* 3.6 30.7 - - + -
51F HIS* 3.8 4.7 - + - -
75F ALA* 3.9 15.9 - - + -
76F MET 3.5 11.0 - - - -
77F VAL* 4.8 1.1 - - + -
118F HIS* 3.5 21.3 - + - -
119F GLY* 3.5 4.2 - - - -
120F SER* 3.1 35.7 + - - +
126F ALA* 4.5 0.2 - - - +
129F GLU* 3.5 25.1 - - + +
130F ILE* 4.1 12.9 - - + +
133F TRP* 3.4 56.1 - + + -
134F PHE* 4.0 12.3 - + - -
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Residues in contact with ILE 9 (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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7F THR* 4.0 20.2 - - + +
8F PHE* 1.3 84.0 - - - +
10F ALA* 1.3 65.6 + - - +
28F PHE* 4.1 26.9 - - + -
74F VAL 3.8 0.2 - - - +
75F ALA* 3.7 0.5 - - - -
76F MET* 2.8 54.0 + - + +
78F TRP* 3.8 27.8 - - + -
87F GLY* 5.1 7.0 - - - -
91F LEU* 4.9 5.4 - - + -
117F ILE* 3.8 21.3 - - + -
118F HIS 3.3 6.7 - - - +
119F GLY* 3.9 15.0 - - - -
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Residues in contact with ALA 10 (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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8F PHE* 3.6 26.0 - - + -
9F ILE* 1.3 76.4 - - - +
11F ILE* 1.3 63.3 + - - +
12F LYS* 3.5 1.1 + - - +
68F MET* 5.6 6.1 - - + -
73F VAL* 4.5 15.3 - - + -
74F VAL 3.2 8.5 - - - +
117F ILE* 3.3 6.5 - - - +
118F HIS* 2.7 47.3 + - + +
133F TRP* 5.3 2.9 - - + -
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Residues in contact with ILE 11 (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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10F ALA* 1.3 72.6 - - - +
12F LYS* 1.3 73.1 + - - +
15F GLY* 3.8 21.1 - - - -
16F VAL* 4.0 6.8 - - + +
21F VAL* 3.9 38.6 - - + +
24F ILE* 4.0 31.6 - - + -
25F ILE* 4.6 2.0 - - + -
73F VAL* 3.4 8.9 - - - +
74F VAL* 2.8 38.2 + - + -
76F MET* 3.7 24.7 - - + -
116F ILE 3.6 10.3 - - - +
117F ILE* 4.5 2.9 - - + +
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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