Contacts of the strand formed by residues 26 - 35 (chain A) in PDB entry 4HXG
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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 2.8 22.6 + - - -
23A ARG* 2.8 21.9 + - + +
24A LYS* 5.7 2.9 - - + -
25A ASN* 1.3 81.8 - - + +
27A VAL* 1.3 62.7 + - - +
47A ILE* 3.8 21.3 - - + -
48A GLU 3.7 7.4 - - - +
49A ASN* 4.6 15.0 - - + +
56A LYS* 4.5 12.3 - - - +
66A ILE* 4.6 13.2 - - + -
70A GLY* 4.1 9.0 - - - +
92A LEU* 3.4 41.3 - - + -
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Residues in contact with VAL 27 (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 ARG 3.3 3.8 - - - +
22A THR* 3.5 13.0 - - - +
26A LEU* 1.3 79.9 - - - +
28A ALA* 1.3 63.8 + - - +
29A TYR* 4.4 4.2 - - + -
46A VAL 3.8 0.3 - - - +
47A ILE* 3.5 2.8 - - - -
48A GLU* 2.6 48.7 + - + +
50A LEU* 3.6 30.5 - - + -
66A ILE* 5.0 0.7 - - - -
313A ILE* 3.4 40.6 - - + -
325A LEU* 3.8 22.4 - - + -
335A LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 28 (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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19A ASP 3.8 0.7 - - - +
20A PRO* 3.6 0.5 - - - +
21A ARG* 2.9 35.9 + - + +
27A VAL* 1.3 76.3 - - - +
29A TYR* 1.3 64.4 + - - +
45A ILE* 4.6 0.7 - - + -
46A VAL 3.3 9.9 - - - +
47A ILE* 3.8 20.9 - - + -
64A PRO* 4.3 20.4 - - + -
66A ILE* 4.3 17.1 - - + +
73A ILE* 4.5 2.9 - - + -
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Residues in contact with TYR 29 (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 LEU* 4.3 18.4 - - + -
18A SER 3.8 9.0 - - - +
19A ASP 3.8 8.1 - - - -
20A PRO* 4.2 12.3 - - + -
27A VAL* 4.4 2.7 - - + -
28A ALA* 1.3 80.0 - - - +
30A VAL* 1.3 75.2 + - - +
31A LEU* 4.8 1.1 - - + -
45A ILE* 3.6 6.1 - - - +
46A VAL* 3.0 52.8 + - + +
48A GLU* 2.9 32.5 + - + -
55A ARG* 3.8 0.2 + - - -
64A PRO* 4.6 2.5 - - - -
315A LEU* 5.4 4.9 - - + -
325A LEU* 3.8 29.8 - - + -
336A THR* 4.0 4.6 - - + +
338A TYR* 2.6 43.8 + + - -
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Residues in contact with VAL 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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16A TYR 3.4 2.6 - - - +
17A LEU* 3.2 7.3 - - - -
18A SER* 2.8 56.2 + - - +
19A ASP* 4.2 4.7 - - + -
29A TYR* 1.3 79.6 - - - +
31A LEU* 1.3 65.0 + - - +
32A THR* 3.7 18.6 - - - +
43A ASN* 4.2 16.2 - - + +
44A THR 3.8 5.8 - - - +
45A ILE* 4.6 2.5 - - + -
61A ALA 4.6 1.1 - - - +
62A SER* 4.3 12.1 - - - -
63A MET 4.3 7.9 - - - +
64A PRO* 3.6 27.4 - - + -
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Residues in contact with LEU 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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15A ALA* 3.6 32.3 - - + -
16A TYR 3.8 1.3 - - - -
17A LEU* 3.8 16.6 - - + -
29A TYR* 4.0 4.0 + - + -
30A VAL* 1.3 72.4 - - - +
32A THR* 1.3 66.9 + - - +
33A LYS* 4.7 7.4 - - + -
42A GLU 3.8 0.3 - - - +
43A ASN* 3.6 2.8 - - - -
44A THR* 2.9 48.1 + - - +
46A VAL* 4.1 17.0 - - + -
338A TYR* 4.2 12.6 - - + -
98B LYS* 4.0 12.8 - - + +
160B GLU 4.0 8.1 - - - +
161B GLY 6.0 0.2 - - - +
162B GLU* 3.7 25.6 - - - +
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Residues in contact with THR 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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15A ALA* 4.1 0.2 - - - -
16A TYR* 2.8 54.3 + - + +
18A SER* 4.7 4.0 + - - -
30A VAL* 3.7 10.6 + - - +
31A LEU* 1.3 76.1 - - - +
33A LYS* 1.3 68.8 + - - +
41A TYR* 4.0 28.3 - - + -
42A GLU 3.3 4.7 - - - +
43A ASN* 2.7 24.4 + - - +
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Residues in contact with LYS 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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12A THR 3.7 7.1 + - - -
13A LYS 4.6 0.2 - - - -
14A PHE 3.3 26.9 - - - +
15A ALA* 4.0 8.5 - - + -
16A TYR* 5.0 0.9 - - - -
31A LEU* 4.4 10.7 + - + -
32A THR* 1.3 80.9 - - - +
34A ALA* 1.3 64.7 + - - +
35A ASN* 3.7 1.0 + - - -
41A TYR* 3.5 6.7 - - - -
42A GLU* 2.9 48.3 + - + +
161B GLY 2.8 27.1 - - - +
162B GLU* 3.6 24.4 + - - +
163B GLU* 2.9 31.8 + - - -
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Residues in contact with ALA 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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11A PHE* 4.4 11.9 - - + +
12A THR* 3.3 50.9 + - + +
14A PHE 5.1 2.0 + - - -
16A TYR* 5.2 5.9 - - + -
33A LYS* 1.3 76.6 + - - +
35A ASN* 1.3 62.3 + - - +
36A LEU 3.5 1.0 + - - -
40A LYS 4.3 0.4 - - - -
41A TYR* 4.1 24.5 - - + -
586A PRO* 4.3 8.7 - - + -
589A ARG* 5.2 0.7 - - - +
163B GLU* 5.5 0.3 - - - +
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Residues in contact with ASN 35 (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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33A LYS* 3.7 2.0 + - + -
34A ALA* 1.3 70.3 - - - +
36A LEU* 1.3 57.8 + - - +
37A GLU* 2.9 15.7 + - - +
38A SER* 2.7 43.4 + - - +
39A ASN* 3.0 20.6 + - - -
40A LYS 3.0 24.1 + - - +
42A GLU* 2.9 33.0 + - - +
586A PRO* 3.5 4.0 - - - +
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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