Contacts of the helix formed by residues 59 - 69 (chain C) 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 PRO 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C ASP 3.8 2.4 - - - +
58C ARG* 1.3 91.6 - - + +
60C PHE* 1.3 64.7 + - + +
61C PHE 3.2 0.2 - - - -
62C PRO* 3.2 18.7 - - - +
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Residues in contact with PHE 60 (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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55C LEU* 4.3 22.2 - - + -
58C ARG* 3.7 44.6 - - + -
59C PRO* 1.3 80.5 - - + +
61C PHE* 1.3 67.3 + - - +
62C PRO* 3.5 1.6 - - - -
63C GLY* 3.3 5.1 + - - +
64C LEU* 3.0 26.6 + - + +
160C GDP 3.6 88.1 + + + +
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Residues in contact with PHE 61 (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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49C LYS* 4.1 28.3 - - + -
52C TYR* 3.3 35.7 - - + -
55C LEU* 3.3 30.7 - - + +
56C LYS* 3.5 31.6 - - + +
58C ARG* 3.1 17.5 + - + +
60C PHE* 1.3 82.8 - - + +
62C PRO* 1.3 74.5 - - + +
64C LEU* 3.0 9.8 + - + +
65C VAL* 3.0 44.0 + - + +
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Residues in contact with PRO 62 (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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58C ARG 4.1 2.0 - - - +
59C PRO 3.2 17.0 - - - +
61C PHE* 1.3 102.1 - - + +
63C GLY* 1.3 57.9 + - - +
65C VAL* 3.5 5.3 + - + +
66C LYS* 3.0 40.6 + - + +
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Residues in contact with GLY 63 (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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60C PHE* 3.3 6.5 + - - +
61C PHE 3.2 0.6 - - - -
62C PRO* 1.3 78.6 - - - +
64C LEU* 1.3 65.2 + - - +
66C LYS* 3.7 7.9 - - - +
67C TYR* 3.1 25.6 + - - +
114C ARG* 5.5 0.5 + - - -
160C GDP 6.4 0.2 - - - -
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Residues in contact with LEU 64 (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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52C TYR* 3.8 41.3 - - + +
55C LEU* 4.1 10.3 - - + -
60C PHE* 3.0 22.0 + - + +
61C PHE* 3.0 15.2 + - + +
63C GLY* 1.3 73.0 - - - +
65C VAL* 1.3 60.9 + - + +
67C TYR* 3.3 13.7 + - + -
68C MET* 2.9 49.5 + - + +
160C GDP 3.4 47.5 + - - +
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Residues in contact with VAL 65 (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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45C GLU* 3.9 45.5 - - + +
48C LEU* 4.0 11.9 - - + +
49C LYS* 4.4 13.9 - - + -
52C TYR* 5.4 2.2 - - + -
61C PHE* 3.0 47.7 + - + +
62C PRO* 3.8 5.2 - - + +
64C LEU* 1.3 78.1 - - + +
66C LYS* 1.3 64.8 + - + +
68C MET* 3.3 6.7 + - - +
69C ASN* 3.1 22.2 + - - +
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Residues in contact with LYS 66 (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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45C GLU* 2.9 30.3 + - - +
62C PRO* 3.0 34.3 + - + +
63C GLY* 3.7 8.1 - - - +
64C LEU 3.2 0.2 - - - -
65C VAL* 1.3 77.5 - - + +
67C TYR* 1.3 61.8 + - - +
69C ASN* 3.2 8.5 + - - +
70C SER* 3.1 21.9 + - - -
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Residues in contact with TYR 67 (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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149A TRP* 4.5 5.4 - + - -
12C LYS* 3.3 22.5 - - + +
13C PRO* 3.5 14.5 - - + +
14C ASP* 2.5 39.5 + - + -
63C GLY 3.1 14.6 + - - +
64C LEU* 3.8 22.0 - - + -
66C LYS* 1.3 72.7 - - - +
68C MET* 1.3 82.6 + - + +
70C SER* 2.6 31.8 + - - -
113C GLY 3.3 20.4 - - - -
114C ARG* 3.5 39.7 - - - +
115C ASN 3.8 8.1 + - - -
160C GDP 4.6 3.4 - - - -
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Residues in contact with MET 68 (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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10C ALA* 5.7 4.3 - - + -
12C LYS* 3.7 38.8 - - + -
13C PRO* 3.6 15.5 - - - +
43C ALA* 4.8 3.3 + - - +
48C LEU* 3.7 38.4 - - + +
51C HIS* 5.4 3.8 - - + +
52C TYR* 4.0 22.2 - - + +
64C LEU* 2.9 36.2 + - + +
65C VAL* 3.8 1.8 - - - +
67C TYR* 1.3 82.5 - - + +
69C ASN* 1.3 58.3 + - - +
71C GLY 3.6 12.8 - - - +
73C VAL* 4.3 23.9 - - + +
118C HIS* 5.6 2.9 - - + -
133C TRP* 5.4 4.7 - - + -
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Residues in contact with ASN 69 (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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42C ARG* 3.2 29.5 + - - +
43C ALA 2.8 25.6 + - - -
44C SER* 4.0 8.3 - - - +
45C GLU* 4.1 22.4 - - + +
48C LEU* 3.8 10.8 - - + -
65C VAL 3.1 15.0 + - - +
66C LYS* 3.7 6.4 - - - +
67C TYR 3.1 0.6 - - - -
68C MET* 1.3 75.7 - - - +
70C SER* 1.3 61.3 + - - +
71C GLY 3.1 7.5 + - - -
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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