Contacts of the helix formed by residues 60 - 72 (chain A) in PDB entry 1NUS
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 ALA 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASP* 3.8 11.0 - - - +
58A LEU 3.8 1.2 + - - -
59A ALA* 1.3 75.6 - - - +
61A SER* 1.3 66.1 + - - +
62A HIS* 4.1 10.3 - - + +
63A HIS* 2.9 34.7 + - + +
64A ARG 3.2 8.3 + - - -
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 5.6 0.2 - - - -
49A VAL 4.3 0.7 - - - -
51A ASP* 2.9 27.5 + - - -
60A ALA* 1.3 71.7 - - - +
62A HIS* 1.3 64.7 + - - +
64A ARG* 3.5 24.7 - - - +
65A VAL* 2.9 29.6 + - - +
85A SER* 3.6 37.8 + - - -
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA* 3.1 9.1 - - + +
61A SER* 1.3 82.1 + - - +
63A HIS* 1.3 78.1 + + + +
65A VAL* 3.9 5.2 - - - +
66A ALA* 3.2 28.2 + - + +
226A TYR* 4.0 6.7 + - - -
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Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ALA* 4.6 3.1 - - + -
60A ALA* 2.9 32.5 + - + +
62A HIS* 1.3 87.9 - + - +
64A ARG* 1.3 59.4 + - - +
66A ALA* 3.3 1.6 + - - +
67A MET* 2.8 38.8 + - + +
226A TYR* 2.6 32.7 + + + -
230A HIS* 4.6 13.7 - + + -
232A LEU* 3.6 44.5 - - + +
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER 3.0 27.0 + - - +
15A PHE* 3.4 19.8 - - - +
16A ASN* 3.7 21.5 - - - +
18A ILE* 5.8 0.3 - - - +
48A PRO* 3.7 18.0 - - + +
49A VAL* 2.9 43.2 + - - +
51A ASP* 2.7 28.5 + - - +
58A LEU* 3.7 17.6 - - - +
59A ALA* 2.8 19.8 + - + +
60A ALA 3.2 4.9 + - - +
61A SER* 3.1 15.3 + - - +
63A HIS* 1.3 73.8 - - - +
65A VAL* 1.3 64.9 + - - +
67A MET* 3.5 17.5 + - + +
68A ALA* 3.1 24.4 + - - +
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 4.1 15.5 - - + -
61A SER 2.9 20.3 + - - +
62A HIS* 3.9 5.6 - - - +
64A ARG* 1.3 75.2 - - - +
66A ALA* 1.3 58.3 + - - +
68A ALA* 3.3 2.9 + - - +
69A ARG* 2.9 51.4 + - - +
80A VAL* 3.8 17.8 - - + +
82A PRO* 3.8 28.5 - - + -
85A SER* 3.5 22.7 - - - +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 3.2 19.5 + - + +
63A HIS 3.5 5.4 - - - +
64A ARG 3.3 0.2 - - - -
65A VAL* 1.3 79.3 - - - +
67A MET* 1.3 63.9 + - - +
69A ARG* 3.2 17.0 + - - +
70A LEU* 2.9 31.0 + - + +
226A TYR* 3.6 31.0 - - + +
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Residues in contact with MET 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE 4.8 0.2 - - - +
17A PRO* 3.8 18.2 - - + -
18A ILE* 4.2 7.2 - - + +
59A ALA* 4.9 0.2 - - + -
63A HIS* 2.8 35.8 + - + +
64A ARG* 3.8 15.5 - - + +
66A ALA* 1.3 70.8 - - - +
68A ALA* 1.3 58.3 + - - +
70A LEU* 3.3 8.1 + - - +
71A ALA* 2.8 30.1 + - - +
223A VAL* 3.4 21.6 - - + +
226A TYR* 3.6 20.6 - - + -
227A ILE* 3.6 30.1 - - - -
232A LEU* 4.2 11.4 - - + -
233A TYR* 3.5 25.6 - - + +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 5.6 1.3 - - + -
18A ILE* 4.1 21.0 - - + +
46A ILE* 4.0 18.2 - - + -
48A PRO* 4.9 1.6 - - + -
64A ARG 3.1 17.4 + - - +
65A VAL 3.6 4.0 - - - +
67A MET* 1.3 73.8 - - - +
69A ARG* 1.3 67.7 + - - +
71A ALA* 3.1 1.6 + - - +
72A LEU* 2.9 31.3 + - + +
80A VAL* 3.8 21.8 - - + -
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 2.9 36.7 + - - +
66A ALA* 3.5 19.0 - - - +
68A ALA* 1.3 77.8 - - - +
70A LEU* 1.3 67.3 + - + +
72A LEU* 3.2 12.6 + - - +
73A GLN* 3.3 24.5 + - - +
80A VAL* 3.8 20.2 + - + +
82A PRO* 5.1 9.3 - - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ALA* 2.9 20.3 + - + +
67A MET* 3.7 4.5 - - - +
69A ARG* 1.3 82.0 - - + +
71A ALA* 1.3 63.3 + - - +
73A GLN* 3.3 24.6 + - + +
74A THR* 6.0 0.5 - - - +
222A ALA* 3.7 36.5 - - + +
226A TYR* 3.6 44.9 - - + +
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 3.8 17.5 - - + -
23A LEU* 4.2 13.8 - - + +
67A MET 2.8 20.7 + - - +
68A ALA* 3.5 4.9 - - - +
70A LEU* 1.3 74.0 - - - +
72A LEU* 1.3 62.6 + - + +
73A GLN 3.3 1.7 + - - -
74A THR* 4.2 12.1 + - - +
75A SER* 5.2 0.5 + - - -
220A PRO* 3.9 20.3 - - + +
222A ALA* 4.9 0.2 - - - -
223A VAL* 3.6 19.6 - - + +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.8 0.4 - - + -
23A LEU* 3.3 32.1 - - + -
46A ILE* 4.0 19.5 - - + -
68A ALA* 2.9 23.7 + - + +
69A ARG* 3.7 6.1 - - - +
70A LEU 3.2 0.4 - - - -
71A ALA* 1.3 76.8 - - + +
73A GLN* 1.3 64.9 + - - +
74A THR 3.2 2.7 - - - -
75A SER* 3.0 28.1 + - - +
78A ILE* 3.5 33.4 - - + +
79A ARG* 3.6 32.5 - - - -
80A VAL* 3.7 5.2 - - - +
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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