Contacts of the helix formed by residues 59 - 68 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D ASP 4.1 3.6 - - - +
58D ARG* 1.3 104.8 - - + +
60D PHE* 1.3 62.7 + - + +
62D PRO* 3.4 12.3 - - - +
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 4.0 25.1 - - + -
58D ARG* 3.8 48.7 - - + -
59D PRO* 1.3 82.0 - - + +
61D PHE* 1.3 69.0 + - - +
62D PRO* 3.3 1.1 - - - -
63D GLY* 3.1 6.8 + - - +
64D LEU* 3.1 27.2 + - + +
160D GDP 3.6 81.4 - + + +
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Residues in contact with PHE 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LYS* 3.8 39.7 - - + -
52D TYR* 3.2 36.3 - - + -
55D LEU* 3.3 28.9 - - + +
56D LYS* 3.7 29.2 - - + +
58D ARG* 3.1 17.5 + - + +
60D PHE* 1.3 84.3 - - - +
62D PRO* 1.3 72.8 - - + +
64D LEU* 3.5 6.3 + - + +
65D VAL* 3.2 36.2 + - + +
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Residues in contact with PRO 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LYS 5.7 0.2 - - - +
58D ARG 4.1 2.5 - - - +
59D PRO* 3.4 17.0 - - + +
60D PHE 3.4 1.3 - - - -
61D PHE* 1.3 102.2 - - + +
63D GLY* 1.3 61.4 + - - +
65D VAL* 3.5 5.1 + - + +
66D LYS* 3.2 32.8 + - + +
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Residues in contact with GLY 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE* 3.1 7.0 + - - +
62D PRO* 1.3 78.0 - - - +
64D LEU* 1.3 59.3 + - - +
66D LYS* 3.9 7.3 - - - +
67D TYR* 3.1 29.3 + - - +
114D ARG* 5.0 1.6 + - - -
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LYS* 5.0 0.2 - - - +
52D TYR* 3.6 48.0 - - + +
55D LEU* 4.0 12.3 - - + -
60D PHE* 3.1 23.5 + - + +
61D PHE* 3.7 14.4 - - + +
63D GLY* 1.3 77.8 - - - +
65D VAL* 1.3 59.1 + - - +
67D TYR* 3.4 13.7 + - + +
68D MET* 3.0 42.3 + - + +
160D GDP 3.7 41.7 - - - +
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLU* 3.7 45.3 - - + +
48D LEU* 3.7 13.7 - - + +
49D LYS* 4.2 17.0 - - + +
52D TYR* 5.4 2.0 - - + -
61D PHE* 3.2 45.4 + - + +
62D PRO* 4.0 5.6 - - + +
64D LEU* 1.3 82.0 - - + +
66D LYS* 1.3 61.7 + - - +
68D MET* 3.3 4.6 + - - -
69D ASN* 3.1 21.7 + - - +
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLU* 2.8 38.7 + - - +
62D PRO* 3.2 21.0 + - + +
63D GLY* 4.0 7.9 - - - +
65D VAL* 1.3 75.5 - - - +
67D TYR* 1.3 63.5 + - - +
69D ASN* 3.5 6.7 + - - +
70D SER* 3.2 22.9 + - - -
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Residues in contact with TYR 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LYS* 3.5 21.6 - - + +
13D PRO* 3.7 11.9 - - + +
14D ASP* 2.5 40.7 + - + -
63D GLY 3.1 18.4 + - - +
64D LEU* 3.7 22.0 - - + +
65D VAL 3.2 0.4 - - - -
66D LYS* 1.3 77.8 - - - +
68D MET* 1.3 79.7 + - + +
70D SER* 2.6 30.2 + - - -
113D GLY 3.4 17.9 - - - -
114D ARG* 3.4 47.2 - - - +
115D ASN 3.6 1.2 + - - -
160D GDP 4.8 3.4 - - - -
149F TRP* 4.7 4.5 - + - -
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Residues in contact with MET 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA* 5.6 6.3 - - + -
12D LYS* 3.7 41.5 - - + -
13D PRO* 3.6 20.4 - - - +
43D ALA* 4.9 3.6 + - - +
48D LEU* 3.4 36.7 - - + +
51D HIS* 5.3 4.9 - - + +
52D TYR* 4.0 23.6 - - + +
64D LEU* 3.0 36.0 + - + +
65D VAL* 3.3 2.0 + - - +
67D TYR* 1.3 83.5 - - + +
69D ASN* 1.3 57.8 + - - +
70D SER 3.4 0.2 - - - -
71D GLY 3.7 5.7 - - - +
73D VAL* 4.4 21.7 - - + +
118D HIS* 5.6 1.3 - - + -
133D TRP* 5.5 4.0 - - + -
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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