Contacts of the helix formed by residues 115 - 124 (chain C) in PDB entry 2NUP
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 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.5 24.0 - - + -
17C ALA* 3.9 7.9 - - + -
91C LEU* 3.6 21.3 - - + -
94C GLU* 3.9 13.5 - - + -
95C PHE* 3.9 24.7 - + + -
98C GLN* 5.7 2.9 - - + -
99C HIS* 4.6 13.6 + + + -
112C PHE* 2.9 23.4 + - + +
114C GLU* 1.3 77.0 - - - +
116C ASP* 1.3 63.3 + - - +
117C THR 3.2 1.5 + - - -
118C PHE* 3.4 37.3 + + + +
119C ILE* 3.3 45.8 + - + +
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Residues in contact with ASP 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B PRO* 5.9 1.4 - - - +
503B PRO* 5.1 7.3 - - - +
541B ARG* 3.4 35.6 + - + +
17C ALA* 5.3 0.6 - - - +
18C ALA 2.9 30.2 - - - +
19C SER* 4.3 2.6 - - - -
113C ILE* 2.7 18.3 + - - +
114C GLU 4.3 0.4 - - - -
115C PHE* 1.3 78.1 - - - +
117C THR* 1.3 65.5 + - - +
119C ILE* 3.5 4.9 + - - +
120C GLN* 2.8 50.8 + - - -
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Residues in contact with THR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540B THR* 4.4 17.5 + - - -
541B ARG* 5.2 4.9 - - - +
587B ASN* 4.6 8.1 + - - +
590B GLU* 3.5 24.9 - - - +
114C GLU 3.9 11.3 + - - -
116C ASP* 1.3 74.8 - - - +
118C PHE* 1.3 67.7 + - - +
120C GLN* 3.1 8.3 + - - +
121C LYS* 3.0 35.8 + - - +
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Residues in contact with PHE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ASP* 3.7 17.3 - - + -
91C LEU* 3.9 12.6 - - + -
94C GLU* 2.8 57.2 - - + -
115C PHE* 3.4 31.3 + + + +
116C ASP 3.6 0.2 - - - -
117C THR* 1.3 78.6 - - - +
119C ILE* 1.3 63.7 + - - +
121C LYS* 3.2 23.7 + - + +
122C THR* 2.9 52.9 + - + -
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Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C THR* 4.3 14.1 - - + -
7C ILE* 4.7 2.2 - - + -
17C ALA* 4.1 13.5 - - + +
18C ALA* 3.8 23.8 - - - +
19C SER* 3.5 24.5 - - - +
87C TYR* 3.8 19.0 + - - +
91C LEU* 3.8 14.6 - - + -
115C PHE* 3.3 44.3 + - + +
116C ASP* 3.5 8.3 - - - +
117C THR 3.2 0.4 - - - -
118C PHE* 1.3 76.2 - - - +
120C GLN* 1.3 53.8 + - - +
122C THR* 3.7 1.9 - - - -
123C LYS* 2.7 36.6 + - - +
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Residues in contact with GLN 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B LYS* 4.8 13.3 + - - -
19C SER* 3.3 25.7 + - - +
20C MET 5.8 0.4 - - - +
21C GLN* 3.8 26.5 + - - +
116C ASP* 2.8 41.6 + - - +
117C THR* 3.1 8.4 + - - +
119C ILE* 1.3 72.1 - - - +
121C LYS* 1.3 65.1 + - - +
122C THR 3.1 1.6 - - - -
123C LYS* 3.7 9.7 - - + +
124C LYS* 3.3 27.4 + - - +
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Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590B GLU* 4.0 23.6 + - - -
117C THR* 3.0 26.2 + - - +
118C PHE* 3.2 31.6 - - + +
120C GLN* 1.3 77.0 - - - +
122C THR* 1.3 69.2 + - - +
124C LYS* 4.1 4.9 + - - +
125C LEU* 3.5 24.4 + - + +
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C TYR* 4.2 18.4 - - + +
90C ASP* 4.2 24.0 - - + +
91C LEU* 4.9 2.0 - - + -
118C PHE* 2.9 46.5 + - + -
119C ILE* 3.8 4.0 - - - -
121C LYS* 1.3 77.8 - - - +
123C LYS* 1.3 65.6 + - - +
124C LYS 3.2 2.0 - - - -
125C LEU* 3.1 20.9 + - + +
126C TYR* 3.4 20.0 - - + -
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Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 3.0 51.9 - - + +
4C LEU 3.8 3.8 - - - +
5C THR* 4.0 5.6 + - - -
19C SER* 3.5 38.3 + - - +
21C GLN* 4.7 6.5 - - - +
87C TYR* 3.4 31.6 - - + +
119C ILE* 2.7 22.8 + - - +
120C GLN* 3.4 9.4 + - - +
122C THR* 1.3 78.1 - - - +
124C LYS* 1.3 65.5 + - + +
126C TYR* 3.3 11.3 + - - +
127C ILE* 3.3 29.7 + - + +
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Residues in contact with LYS 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A PRO* 5.7 12.3 - - + +
581B PRO* 4.4 7.7 + - - +
582B GLU* 3.0 56.0 + - - +
21C GLN* 6.3 0.9 - - - +
120C GLN 3.3 14.4 + - - +
121C LYS* 4.1 6.0 + - - +
122C THR 3.2 1.0 - - - -
123C LYS* 1.3 76.9 - - + +
125C LEU* 1.3 62.0 + - + +
126C TYR 2.9 11.2 + - - -
127C ILE* 3.3 19.4 + - + +
128C ASP* 4.1 9.2 - - - +
131C ALA* 5.6 0.5 - - - +
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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