Contacts of the strand formed by residues 30 - 37 (chain E) in PDB entry 1NVI
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 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E ASP 3.3 0.8 - - - +
29E GLY* 1.3 77.8 - - - +
31E VAL* 1.3 63.5 + - - +
32E VAL* 4.3 1.8 - - + -
100E THR* 3.2 9.2 - - - -
101E SER 2.9 32.6 + - - +
103E HIS* 3.6 28.3 - - - +
104E ARG* 3.7 14.6 - - + +
107E ALA* 4.2 7.9 - - + -
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TYR* 3.5 33.9 - - + +
22E LEU* 4.0 28.5 - - + -
23E ALA* 4.2 22.4 - - + -
28E ASP* 4.7 9.2 - - + +
29E GLY 5.4 0.7 - - - -
30E ALA* 1.3 80.0 - - - +
32E VAL* 1.3 67.2 + - - +
33E THR* 4.3 5.4 + - + +
99E VAL 3.5 5.2 - - - +
100E THR* 4.0 12.6 - - + -
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Residues in contact with VAL 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ALA* 4.3 1.5 - - + -
31E VAL* 1.3 77.4 - - - +
33E THR* 1.3 73.4 + - - +
34E PHE* 5.9 1.8 - - + -
97E VAL 3.8 0.7 - - - +
98E GLY* 3.4 2.9 - - - -
99E VAL* 3.0 33.6 + - - +
104E ARG* 4.8 0.9 - - + +
107E ALA* 3.5 42.8 - - + +
108E PHE* 3.7 40.6 - - + +
111E GLY* 5.0 9.4 - - - -
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Residues in contact with THR 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E VAL* 4.8 9.7 - - + +
19E TYR* 4.4 18.4 - - + -
22E LEU* 4.2 12.8 - - + -
31E VAL* 4.3 4.2 + - + +
32E VAL* 1.3 86.6 - - - +
34E PHE* 1.3 62.2 + - - +
35E THR* 5.0 1.9 + - - -
96E PHE* 3.7 33.6 - - + -
97E VAL 3.3 4.3 - - - -
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Residues in contact with PHE 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLY 5.1 1.3 - - - -
32E VAL* 5.9 1.6 - - + -
33E THR* 1.3 74.5 - - - +
35E THR* 1.3 77.6 + - - +
36E GLY* 3.4 23.8 - - - -
95E VAL* 4.0 3.1 - - + -
96E PHE* 3.3 7.6 - - - -
97E VAL* 2.8 40.6 + - + +
111E GLY* 5.5 4.7 - - - +
115E MET* 3.6 50.9 - - + -
151E SO4 4.7 14.6 - - - -
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Residues in contact with THR 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E PHE* 4.2 4.9 - - + -
15E VAL* 3.5 22.6 - - + +
33E THR* 5.0 2.4 + - - -
34E PHE* 1.3 91.8 + - - +
36E GLY* 1.3 60.5 + - - +
37E LYS* 4.2 10.0 + - + +
93E GLU* 3.7 43.3 - - + +
95E VAL 3.3 9.4 - - - +
96E PHE* 3.6 6.2 - - - -
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Residues in contact with GLY 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLY 4.7 4.5 - - - -
34E PHE* 3.4 21.3 - - - -
35E THR* 1.3 73.4 - - - +
37E LYS* 1.3 55.2 + - - -
93E GLU* 3.7 2.6 - - - -
94E ILE* 2.8 38.3 + - - +
95E VAL* 3.0 19.9 + - - +
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Residues in contact with LYS 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E THR* 4.4 11.2 - - + +
36E GLY* 1.3 78.4 - - - +
38E VAL* 1.3 69.2 + - - +
39E ARG* 3.5 11.5 + - + +
91E GLY* 4.4 15.0 - - - +
92E ASP 3.2 13.0 - - - +
93E GLU* 4.0 29.6 - - + +
94E ILE* 3.8 6.5 - - - +
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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