Contacts of the strand formed by residues 29 - 34 (chain A) in PDB entry 2GUX
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 LEU 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.7 31.9 - - + -
24A ARG 3.8 3.6 - - - +
25A SER* 4.3 2.2 - - - -
28A TYR* 1.3 72.1 - - - +
30A ASP* 1.3 59.5 + - - +
31A ALA 4.0 7.0 - - - +
68A TYR* 5.7 0.2 - - - -
69A ILE* 2.9 27.9 + - + +
70A ASP 3.7 2.5 - - - +
71A ASN* 3.6 23.8 - - - +
72A ILE* 3.5 28.5 - - + +
85A TYR 3.5 24.9 - - - +
86A GLY* 4.3 1.8 - - - -
110A TYR* 3.6 8.1 - - - +
111A LEU* 2.9 39.8 + - + +
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Residues in contact with ASP 30 (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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24A ARG* 2.8 12.1 + - + +
25A SER* 3.5 5.2 - - - -
26A GLY* 3.5 23.0 + - - -
28A TYR 3.7 2.3 - - - +
29A LEU* 1.3 72.4 - - - +
31A ALA* 1.3 59.3 + - - +
40A GLY* 3.5 0.7 - - - -
41A GLY 3.0 22.0 + - - +
43A GLY* 3.2 46.3 + - - +
44A GLY* 3.6 3.7 + - - -
109A ASP 4.5 3.7 - - - +
110A TYR* 3.2 50.5 + - - +
111A LEU 3.9 1.1 - - - -
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Residues in contact with ALA 31 (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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23A VAL* 3.3 8.5 - - - +
24A ARG* 2.9 32.5 + - + +
29A LEU* 3.5 3.8 - - - +
30A ASP* 1.3 83.3 - - - +
32A ILE* 1.3 63.3 + - - +
33A ILE* 4.9 0.9 - - + -
38A HIS* 3.6 19.1 - - + +
39A HIS 3.2 13.9 - - - +
40A GLY* 3.8 1.3 - - - -
41A GLY 3.5 19.5 - - - +
111A LEU* 4.4 8.5 - - - +
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Residues in contact with ILE 32 (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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21A ILE* 4.1 17.9 - - + -
22A ALA 3.6 10.1 - - - +
23A VAL* 4.1 5.6 - - + -
31A ALA* 1.3 75.1 - - - +
33A ILE* 1.3 62.1 + - - +
34A ILE* 4.0 21.3 - - + -
39A HIS* 2.7 53.5 + - + +
72A ILE* 4.4 18.8 - - + -
103A ILE* 4.2 28.7 - - + -
111A LEU* 3.8 29.5 - - + +
114A LEU* 4.2 9.4 - - + -
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Residues in contact with ILE 33 (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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20A SER 3.7 0.3 - - - +
21A ILE* 3.2 8.3 - - - +
22A ALA* 2.7 52.4 + - + +
23A VAL 4.1 7.6 - - - +
24A ARG* 4.3 9.4 - - + +
31A ALA* 4.9 0.9 - - + +
32A ILE* 1.3 77.8 - - - +
34A ILE* 1.3 60.4 + - - +
35A ASP 4.1 0.4 + - - -
36A GLY* 3.5 38.1 + - - +
37A VAL 3.2 5.6 - - - +
38A HIS* 3.9 24.9 - - + +
46A LEU* 3.6 30.7 - - + -
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Residues in contact with ILE 34 (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 GLY 5.2 0.7 - - - +
18A LEU* 3.8 28.5 - - + -
20A SER 3.4 3.8 - - - +
21A ILE* 4.8 3.1 - - + -
32A ILE* 4.0 21.0 - - + -
33A ILE* 1.3 76.5 - - - +
35A ASP* 1.3 82.7 + - - +
37A VAL* 2.9 27.9 + - - +
39A HIS* 4.1 23.5 - - + +
102A GLN* 5.0 6.1 - - - +
103A ILE* 3.6 42.0 - - + +
104A ASN 6.1 0.4 - - - -
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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