Contacts of the strand formed by residues 12 - 18 (chain A) in PDB entry 1NVT
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 LYS 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ALA 5.5 1.0 + - - -
10A LYS* 3.3 23.8 - - - +
11A THR* 1.3 81.0 + - - +
13A VAL* 1.3 62.0 + - - +
40A ASN 3.0 10.7 + - - +
41A TYR* 3.2 33.5 - - + +
42A VAL* 2.9 27.4 + - - +
63A LEU 5.9 1.0 + - - -
64A GLY* 4.6 12.9 + - - +
66A VAL* 3.7 20.0 - - + -
45B ALA 4.6 10.5 + - - -
47B ASP* 5.4 11.1 - - - +
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Residues in contact with VAL 13 (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 THR 4.7 3.8 - - - +
12A LYS* 1.3 77.9 - - - +
14A ILE* 1.3 76.1 + - - +
42A VAL* 3.8 15.3 - - + +
44A VAL* 4.0 18.8 - - + -
46A PHE* 4.4 9.2 - - + -
64A GLY 5.0 2.6 + - - -
65A ILE* 3.3 25.1 - - + +
66A VAL* 2.9 30.7 + - - +
13B VAL* 5.9 2.7 - - + -
44B VAL* 4.0 22.0 - - + -
45B ALA 5.7 0.4 - - - +
46B PHE* 3.8 23.1 - - + -
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Residues in contact with ILE 14 (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 VAL* 1.3 83.6 - - - +
15A GLY* 1.3 62.9 + - - +
34A PHE* 3.8 23.8 - - + -
41A TYR* 4.0 19.1 - - + -
42A VAL 3.0 13.4 + - - +
43A TYR* 3.2 30.7 - - + -
44A VAL* 3.1 23.6 + - - +
66A VAL* 4.2 5.4 - - + -
67A GLY 3.4 21.8 - - - +
267A TRP* 3.7 48.0 - - + -
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Residues in contact with GLY 15 (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 VAL* 4.7 0.2 - - - +
14A ILE* 1.3 79.2 - - - +
16A LEU* 1.3 60.8 + - - -
43A TYR* 4.2 6.7 + - - -
44A VAL 3.1 10.8 - - - -
46A PHE* 4.0 17.4 - - - -
67A GLY 3.1 7.9 + - - -
68A PHE* 2.8 15.9 - - - +
69A ASN 2.8 23.3 + - - -
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Residues in contact with LEU 16 (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 GLY* 1.3 73.1 - - - -
17A ILE* 1.3 67.4 + - - +
21A VAL* 3.9 25.1 - - + +
24A SER* 3.4 36.8 - - - +
26A SER* 4.7 4.0 - - - +
27A PRO* 5.3 0.2 - - + -
43A TYR* 3.4 20.8 - - + +
44A VAL 2.9 8.8 + - - +
45A ALA* 4.5 5.6 - - + -
46A PHE* 2.8 30.3 + - - +
69A ASN* 3.4 30.7 - - + +
70A VAL 4.2 0.4 - - - +
71A THR* 4.1 20.9 - - + -
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Residues in contact with ILE 17 (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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16A LEU* 1.3 76.9 - - - +
18A GLY* 1.3 58.6 + - - +
21A VAL* 4.3 2.2 - - - -
46A PHE* 3.6 4.7 - - + -
48A VAL* 4.2 11.9 - - + -
53A LEU* 4.3 12.8 - - + -
56A VAL* 4.5 8.3 - - + -
68A PHE* 3.4 39.7 - - + -
69A ASN 2.8 18.1 + - - +
70A VAL* 3.8 24.5 - - + +
71A THR* 3.0 26.7 + - - +
74A HIS* 4.0 3.6 - - + -
78A ILE* 4.2 23.1 - - + -
98A ILE* 4.9 0.7 - - + -
63B LEU* 4.1 17.5 - - + -
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Residues in contact with GLY 18 (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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17A ILE* 1.3 75.5 - - - +
19A HIS* 1.3 59.9 + - - -
21A VAL* 3.4 14.2 - - - +
46A PHE 3.4 8.1 + - - +
47A ASP* 3.4 3.5 - - - -
48A VAL 2.8 23.8 + - - +
71A THR* 3.9 2.7 - - - -
72A ILE 3.4 10.1 - - - -
74A HIS* 3.3 20.0 - - - -
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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