Contacts of the strand formed by residues 13 - 18 (chain E) in PDB entry 3ALQ
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 VAL 13 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E MET 3.3 9.8 + - - +
12E PRO* 1.3 75.9 - - - +
14E ALA* 1.3 78.3 + - - +
36E LEU* 4.3 18.8 - - + -
37E LEU* 3.7 0.2 - - - -
38E ALA* 3.2 35.4 + - + +
39E ASN* 4.6 4.3 - - - +
41E VAL* 3.4 8.0 - - - +
154E ILE 3.2 14.4 - - - +
155E ILE* 3.7 17.7 - - + -
55F LEU* 3.6 30.3 - - + -
123F VAL* 4.2 12.8 - - + -
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Residues in contact with ALA 14 (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 VAL* 1.3 81.4 - - - +
15E HIS* 1.3 61.5 + - - +
16E VAL* 4.0 2.5 - - + -
36E LEU* 3.4 14.6 - - - +
37E LEU* 3.9 9.2 - - + -
41E VAL* 3.8 21.5 - - + -
48E LEU* 4.2 13.0 - - + -
59E TYR* 4.1 2.1 + - - -
153E GLY* 2.9 4.1 - - - -
154E ILE* 2.8 44.3 + - + +
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Residues in contact with HIS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ALA* 1.3 73.8 - - - +
16E VAL* 1.3 66.0 + - - +
17E VAL* 4.2 9.6 - - + +
34E ASN 3.9 15.3 - - - +
35E ALA* 3.3 6.4 - - - -
36E LEU* 2.9 37.0 + - + +
59E TYR* 2.5 44.5 + + - +
151E TYR* 3.4 29.5 - + + +
152E PHE 3.5 4.5 - - - -
93F LEU 5.0 1.4 + - - -
94F LEU* 4.9 0.2 - - - +
122F GLY* 4.1 1.6 - - - -
123F VAL* 3.5 19.2 + - + +
124F PHE* 3.8 26.7 - + - -
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Residues in contact with VAL 16 (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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14E ALA* 5.0 2.0 - - + -
15E HIS* 1.3 78.1 - - - +
17E VAL* 1.3 58.7 + - - +
28E TRP* 3.5 34.3 - - + -
29E LEU 3.1 16.4 - - - +
30E ASN* 4.3 9.0 - - + +
36E LEU 4.3 5.2 - - - +
37E LEU* 5.1 2.2 - - + -
43E LEU* 3.9 23.6 - - + -
48E LEU* 4.2 16.8 - - + -
151E TYR* 3.4 5.9 - - - +
152E PHE* 2.8 55.3 + - + +
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Residues in contact with VAL 17 (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 HIS* 4.2 21.3 - - + +
16E VAL* 1.3 79.7 - - - +
18E ALA* 1.3 71.3 + - - +
20E PRO* 5.8 0.2 - - + -
28E TRP* 3.5 6.4 - - - -
29E LEU* 2.8 41.3 + - + +
32E ARG* 4.2 26.9 - - + -
33E ALA 5.7 1.6 - - - +
34E ASN 5.3 1.3 - - - +
35E ALA* 4.2 11.4 - - + +
148E GLY* 6.0 5.2 - - - +
150E VAL 3.6 8.7 - - - +
151E TYR* 4.8 2.2 - - + -
73V SER* 4.8 5.4 - - - +
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Residues in contact with ALA 18 (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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17E VAL* 1.3 80.8 - - - +
19E ASN* 1.3 59.4 + - - +
20E PRO* 2.8 19.9 - - - +
26E LEU* 3.8 8.1 - - + -
27E GLN 3.9 4.3 - - - -
28E TRP* 4.1 4.4 - - - -
144E PHE* 3.7 23.1 - - + +
150E VAL* 3.0 44.1 + - + +
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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