Contacts of the strand formed by residues 39 - 48 (chain A) in PDB entry 1NUR
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 TYR 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ARG* 2.8 25.7 + - - +
5A ILE* 3.3 22.6 - - + +
7A VAL* 3.6 23.3 - - + -
33A LEU* 3.7 32.8 + - + +
34A HIS* 3.4 11.9 - - - -
36A THR* 3.5 22.9 - - + -
37A GLY 3.7 0.2 - - - -
38A MET* 1.3 111.8 - - + +
40A GLN* 1.3 61.5 + - - +
129A GLU* 4.0 19.8 + - - -
131A LYS* 4.3 5.9 + - - -
187A HIS 4.8 2.4 + - - -
188A ASN* 5.5 3.3 + - - -
190A HIS* 3.2 37.7 + + - -
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Residues in contact with GLN 40 (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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4A ARG* 4.1 22.8 - - + +
5A ILE 2.9 9.2 + - - +
6A PRO* 3.4 8.3 - - + +
7A VAL* 2.9 20.9 + - - -
34A HIS* 3.6 9.6 - - + +
39A TYR* 1.3 74.9 - - - +
41A VAL* 1.3 65.8 + - - +
42A ILE* 3.3 18.6 + - + +
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Residues in contact with VAL 41 (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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7A VAL* 3.3 15.3 - - + +
9A LEU* 3.7 16.8 - - + -
30A ARG* 3.7 37.0 + - + -
33A LEU* 3.7 36.1 - - + -
34A HIS* 2.9 16.6 + - - +
40A GLN* 1.3 74.8 - - - +
42A ILE* 1.3 61.3 + - - +
43A GLN 3.8 4.0 - - - +
77A TRP* 3.4 34.6 - - + +
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Residues in contact with ILE 42 (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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6A PRO* 4.2 13.7 - - + -
7A VAL 2.8 18.0 + - - +
8A VAL* 4.0 13.0 - - + -
40A GLN* 3.7 29.2 - - + +
41A VAL* 1.3 75.2 - - - +
43A GLN* 1.3 67.4 + - + +
77A TRP* 4.6 10.6 - - - +
104A LEU* 5.9 1.6 - - + -
128A PRO* 4.0 27.1 - - + -
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Residues in contact with GLN 43 (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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7A VAL 3.7 0.2 + - - -
8A VAL* 3.3 14.4 - - + +
9A LEU 2.9 24.8 + - - -
41A VAL* 3.5 7.6 - - - +
42A ILE* 1.3 93.3 + - + +
44A GLY* 1.3 77.9 + - - +
45A ILE* 4.2 8.5 - - + +
77A TRP* 3.4 24.3 + - - +
79A ARG* 3.4 44.1 + - - +
104A LEU* 5.5 5.0 - - - +
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Residues in contact with GLY 44 (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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9A LEU 3.4 6.7 - - - -
26A PHE* 3.8 14.6 - - - -
43A GLN* 1.3 81.2 - - - +
45A ILE* 1.3 64.5 + - - +
77A TRP* 2.9 20.8 + - - -
78A ILE* 3.3 8.6 - - - -
79A ARG* 2.9 23.9 + - - +
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Residues in contact with ILE 45 (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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8A VAL* 3.8 23.6 - - + -
9A LEU 2.8 13.0 + - - +
10A LEU* 3.8 19.1 - - + -
11A ALA 2.8 31.4 + - - +
26A PHE* 3.6 4.9 - - - -
43A GLN* 4.2 8.1 - - - +
44A GLY* 1.3 79.0 - - - +
46A ILE* 1.3 63.3 + - - +
47A SER* 4.8 0.2 - - - -
79A ARG* 3.3 33.9 - - - +
81A ASP* 3.7 28.0 - - + -
100A HIS* 4.0 24.2 - - + +
104A LEU* 6.2 3.1 - - + -
130A LEU* 5.2 1.1 - - + -
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Residues in contact with ILE 46 (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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11A ALA 3.8 2.2 - - - -
15A PHE* 3.7 46.7 - - + -
18A ILE* 3.9 12.6 - - + -
22A HIS 5.3 1.1 - - - +
23A LEU* 5.1 2.0 - - + -
26A PHE* 3.1 35.0 - - + -
45A ILE* 1.3 71.0 - - - +
47A SER* 1.3 58.7 + - - +
48A PRO* 4.2 4.0 - - + -
68A ALA* 4.1 19.1 - - + -
72A LEU* 3.8 23.1 - - + -
78A ILE* 4.0 5.2 - - + -
79A ARG 2.9 10.1 + - - +
80A VAL* 3.3 10.0 - - - +
81A ASP 2.8 31.4 + - - -
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Residues in contact with SER 47 (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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10A LEU* 3.9 20.6 - - - -
11A ALA 2.9 20.0 + - - +
12A CYS* 3.7 12.4 - - - -
13A GLY 3.7 1.7 + - - +
15A PHE* 4.2 1.8 - - - -
45A ILE* 3.9 1.3 + - - -
46A ILE* 1.3 72.4 - - - +
48A PRO* 1.3 66.6 - - - +
49A VAL 3.5 1.4 + - - -
81A ASP 3.7 9.0 + - - -
84A GLU* 2.5 42.6 + - - +
96A VAL* 3.9 5.0 - - - +
100A HIS* 4.3 6.1 + - - -
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Residues in contact with PRO 48 (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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13A GLY 3.5 7.2 - - - +
14A SER 4.3 4.5 - - - +
15A PHE* 3.9 6.3 - - + -
46A ILE* 3.5 20.0 - - + +
47A SER* 1.3 85.5 - - - +
49A VAL* 1.3 65.7 + - - +
50A ASN 3.6 0.2 + - - -
61A SER 5.5 0.2 - - - +
64A ARG* 3.6 28.7 - - + +
65A VAL* 4.1 23.8 - - + -
80A VAL* 3.8 20.6 - - + -
81A ASP 3.8 7.9 - - - +
82A PRO* 5.1 0.9 - - + -
84A GLU* 3.8 4.2 - - - +
85A SER* 3.5 21.1 + - - -
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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