Contacts of the helix formed by residues 61 - 69 (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 PHE 61 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49F LYS* 4.0 33.4 - - + -
52F TYR* 3.3 35.4 - - + -
55F LEU* 3.2 31.0 - - + +
56F LYS* 3.6 30.7 - - + +
58F ARG* 3.1 19.3 + - + +
60F PHE* 1.3 85.2 - - - +
62F PRO* 1.3 72.8 - - + +
64F LEU* 3.2 6.4 + - + +
65F VAL* 3.0 47.8 + - + +
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Residues in contact with PRO 62 (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 GLU* 4.7 1.7 - - - +
56F LYS 6.0 0.2 - - - +
58F ARG 3.9 3.1 - - - +
59F PRO 3.4 15.3 - - - +
60F PHE 3.6 0.7 - - - -
61F PHE* 1.3 103.9 - - + +
63F GLY* 1.3 56.0 + - - +
65F VAL* 3.5 5.4 + - + +
66F LYS* 3.0 35.3 + - + +
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Residues in contact with GLY 63 (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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59F PRO 5.3 0.2 + - - -
60F PHE* 3.1 6.9 + - - +
62F PRO* 1.3 77.6 - - - +
64F LEU* 1.3 65.8 + - - +
66F LYS* 3.2 9.0 + - - +
67F TYR* 3.0 24.6 + - - +
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Residues in contact with LEU 64 (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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52F TYR* 4.0 37.0 - - + +
55F LEU* 4.1 6.1 - - + -
60F PHE* 2.9 31.4 + - + +
61F PHE* 3.4 13.7 - - + +
63F GLY* 1.3 75.4 - - - +
65F VAL* 1.3 63.3 + - + +
67F TYR* 3.1 18.3 + - + +
68F MET* 2.9 42.2 + - + +
160F GDP 3.5 43.9 + - - +
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Residues in contact with VAL 65 (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 GLU* 3.6 45.1 - - + +
48F LEU* 3.9 15.4 - - + +
49F LYS* 4.2 12.3 - - + -
52F TYR* 5.4 2.2 - - + -
61F PHE* 3.0 49.1 + - + +
62F PRO* 3.8 5.2 - - + +
64F LEU* 1.3 78.8 - - + +
66F LYS* 1.3 63.1 + - - +
68F MET* 3.3 6.3 + - - +
69F ASN* 3.0 26.2 + - - +
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Residues in contact with LYS 66 (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 GLU* 4.0 25.0 + - - +
62F PRO* 3.0 28.5 + - - +
63F GLY* 3.4 11.4 - - - +
64F LEU 3.2 0.2 - - - -
65F VAL* 1.3 75.4 - - - +
67F TYR* 1.3 57.7 + - - +
69F ASN* 3.2 8.7 + - - +
70F SER* 3.0 26.3 + - - -
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Residues in contact with TYR 67 (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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149E TRP* 4.5 4.9 - + - -
12F LYS* 3.5 21.2 - - + +
13F PRO* 3.4 12.9 - - + +
14F ASP* 2.5 40.2 + - + -
63F GLY 3.0 11.1 + - - +
64F LEU* 3.7 25.1 - - + -
66F LYS* 1.3 76.7 - - - +
68F MET* 1.3 76.8 + - + +
69F ASN 3.0 1.8 - - - -
70F SER* 2.6 31.4 + - - -
113F GLY 3.3 20.9 - - - -
114F ARG* 3.6 44.5 - - - +
115F ASN 3.7 2.1 + - - -
160F GDP 4.9 3.1 - - - -
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Residues in contact with MET 68 (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* 5.6 4.0 - - + -
12F LYS* 3.6 40.4 - - + -
13F PRO* 3.7 15.1 - - - +
43F ALA* 4.7 4.3 + - - +
48F LEU* 3.5 37.2 - - + +
51F HIS* 5.5 1.8 - - + +
52F TYR* 3.9 23.1 - - + +
64F LEU* 2.9 34.8 + - + +
65F VAL* 3.9 2.5 - - - +
67F TYR* 1.3 82.5 - - + +
69F ASN* 1.3 58.9 + - - +
71F GLY 3.7 11.6 - - - +
73F VAL* 4.4 21.5 - - + +
118F HIS* 5.6 3.6 - - + -
133F TRP* 5.4 6.3 - - + -
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Residues in contact with ASN 69 (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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42F ARG* 3.2 28.7 + - - +
43F ALA 2.7 26.1 + - - -
44F SER* 3.9 8.7 - - - +
45F GLU* 4.0 20.2 - - + +
48F LEU* 3.7 9.9 - - + -
65F VAL 3.0 15.9 + - - +
66F LYS* 3.5 5.7 - - - +
67F TYR 3.0 0.6 - - - -
68F MET* 1.3 78.2 - - - +
70F SER* 1.3 62.4 + - - +
71F GLY 3.2 5.9 + - - -
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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