Contacts of the helix formed by residues 26 - 34 (chain A) in PDB entry 4UHX
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 MET 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PRO 5.2 0.4 - - - +
24A GLU* 3.4 23.2 + - - +
25A THR* 1.3 75.6 - - - +
27A LEU* 1.3 65.3 + - - +
28A LEU 3.4 0.4 - - - +
29A PRO* 3.5 24.2 - - + +
30A TYR* 3.1 22.3 + - - +
74A CYS 4.1 17.7 - - - +
75A LEU* 4.3 8.5 - - - +
76A ILE 3.5 16.2 - - - +
77A PRO* 3.8 22.4 - - + -
78A ILE* 3.8 2.2 - - - -
268A ASN* 4.4 12.3 - - - +
272A GLY* 6.3 0.4 - - - -
275A VAL* 5.9 6.5 - - + -
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Residues in contact with LEU 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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9A PHE* 4.7 7.6 - - + -
26A MET* 1.3 69.8 - - - +
28A LEU* 1.3 60.5 + - - +
30A TYR* 4.8 4.5 - - + -
31A LEU* 2.8 61.3 + - + +
54A VAL* 4.1 9.4 - - + -
56A ILE* 4.7 0.2 - - + -
73A ALA* 3.6 23.5 + - + +
76A ILE* 2.9 37.3 + - + +
78A ILE* 3.6 14.7 - - + +
81A LEU* 3.8 26.7 - - + -
86A VAL* 4.1 20.0 - - + -
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Residues in contact with LEU 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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27A LEU* 1.3 78.7 - - - +
29A PRO* 1.4 72.4 - - + +
31A LEU* 3.6 3.9 + - - +
32A ARG* 3.3 49.2 + - + +
40A THR* 3.7 26.7 - - + +
41A LYS 3.8 21.1 - - - +
42A TYR* 4.0 25.8 - - + -
52A CYS* 4.1 3.8 - - + -
73A ALA* 3.3 9.6 + - + -
74A CYS* 3.8 37.7 - - + +
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Residues in contact with PRO 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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25A THR* 5.6 2.5 - - + -
26A MET* 3.5 28.7 - - + +
28A LEU* 1.4 97.3 - - + +
30A TYR* 1.3 55.2 + - - +
32A ARG* 3.3 4.4 + - + -
33A LYS* 2.8 51.2 + - + +
74A CYS* 5.5 1.3 - - - +
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Residues in contact with TYR 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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9A PHE* 3.9 22.4 - + - -
16A VAL* 3.2 21.2 - - + +
17A ILE 5.0 0.2 + - - -
18A GLU* 2.7 40.8 + - + +
25A THR* 4.0 12.3 - - + +
26A MET 3.1 17.1 + - - +
27A LEU* 3.2 8.9 + - + +
29A PRO* 1.3 78.1 - - - +
31A LEU* 1.3 60.9 + - - +
34A LYS* 2.9 52.0 + - + +
35A LEU* 3.0 40.1 + - + +
78A ILE* 4.0 26.0 - - + -
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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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11A VAL* 3.7 31.2 - - + -
27A LEU* 2.8 55.1 + - + +
28A LEU* 3.8 3.6 - - - +
30A TYR* 1.3 73.9 - - - +
32A ARG* 1.3 58.9 + - + +
35A LEU* 3.4 14.3 - - + +
36A ARG 3.1 10.7 + - - -
37A LEU* 2.8 38.7 + - + +
40A THR* 4.1 15.0 - - + +
54A VAL* 4.3 8.7 - - + -
73A ALA* 4.4 3.8 - - + -
86A VAL* 4.7 2.7 - - + -
88A THR* 3.9 21.3 - - - +
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Residues in contact with ARG 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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28A LEU* 3.3 32.3 + - + +
29A PRO* 4.0 3.8 - - + +
31A LEU* 1.3 77.4 - - + +
33A LYS* 1.3 66.7 + - + +
36A ARG* 3.4 20.3 - - - +
37A LEU 3.7 13.5 - - - +
38A THR* 2.8 44.4 + - + +
40A THR 3.1 23.2 + - - +
41A LYS* 4.1 9.5 - - - +
42A TYR* 5.0 6.9 - - - +
601A ASP* 2.8 44.6 + - - +
602A ASP* 2.7 21.8 + - - +
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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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29A PRO* 2.8 32.1 + - + +
30A TYR* 5.4 0.2 - - - -
32A ARG* 1.3 81.4 - - + +
34A LYS* 1.3 62.5 + - - +
36A ARG* 3.5 23.6 + - - -
601A ASP* 5.7 7.9 - - - -
605A LEU* 6.5 0.9 - - + -
611A PHE* 5.4 4.2 - - - -
683A GLU* 3.0 37.3 + - - +
833A ARG* 6.4 2.2 - - - +
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Residues in contact with LYS 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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18A GLU* 2.9 28.8 + - - -
29A PRO 4.0 0.2 + - - -
30A TYR* 2.9 49.8 + - + +
33A LYS* 1.3 76.4 - - + +
35A LEU* 1.3 64.7 + - + +
36A ARG* 2.7 29.3 + - - +
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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