Contacts of the strand formed by residues 52 - 57 (chain A) in PDB entry 3HMX
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 THR 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL* 2.9 32.7 - - + +
26A LEU 3.2 6.7 + - - -
27A THR* 4.2 10.1 + - - +
38A TRP* 4.3 0.2 - - - -
49A SER 3.6 13.7 - - - +
50A GLY* 2.8 9.8 - - - +
51A LYS* 1.3 81.9 - - - +
53A LEU* 1.3 60.0 + - - +
54A THR* 4.3 6.9 + - - +
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Residues in contact with LEU 53 (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 VAL 3.7 1.6 - - - +
25A VAL* 3.6 1.9 - - - -
26A LEU* 2.7 41.6 + - + +
38A TRP* 3.6 47.5 - - + +
47A LEU* 4.3 15.9 - - + +
48A GLY* 4.1 29.8 - - - +
49A SER 4.7 1.6 - - - +
52A THR* 1.3 74.7 - - - +
54A THR* 1.3 69.5 + - - +
55A ILE* 3.7 21.1 + - + +
66A TYR* 4.4 11.9 - - + -
100H ARG* 5.1 2.5 - - - +
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A MET* 3.8 30.5 - - + -
24A VAL 3.5 3.1 - - - +
25A VAL* 3.7 29.7 - - + +
52A THR* 4.2 6.8 - - - +
53A LEU* 1.3 80.4 - - - +
55A ILE* 1.3 67.0 - - - +
100H ARG* 5.5 0.5 + - - -
103H GLN* 3.7 11.1 - - - +
32L TRP* 5.0 4.0 - - + -
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Residues in contact with ILE 55 (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 MET* 3.4 6.8 - - - +
24A VAL* 2.9 47.3 + - + +
26A LEU* 4.3 9.9 - - + -
53A LEU* 3.8 30.7 - - + +
54A THR* 1.3 80.3 - - - +
56A GLN* 1.3 60.6 + - - +
57A VAL* 3.8 18.6 - - + -
66A TYR* 3.4 39.7 - - + +
80A LEU* 4.6 3.1 - - + -
100H ARG* 4.9 6.7 - - - +
102H GLY* 3.2 21.1 - - - +
103H GLN* 4.1 2.5 - - - -
32L TRP* 3.7 8.1 - - - -
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Residues in contact with GLN 56 (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 GLY* 4.1 15.5 + - - -
22A GLU 3.3 6.7 - - - +
55A ILE* 1.3 74.5 - - - +
57A VAL* 1.3 72.3 + - - +
58A LYS* 3.7 21.7 - - + +
62A ASP* 3.5 6.0 - - - +
102H GLY* 2.8 29.5 + - - +
103H GLN 3.7 21.7 + - - +
32L TRP* 3.0 59.1 - - + +
91L TYR 3.5 15.9 + - - +
92L ASN* 4.2 3.4 - - - +
96L TYR* 4.1 4.2 + - - -
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Residues in contact with VAL 57 (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* 3.8 28.0 - - + -
13A LEU* 3.4 11.1 - - + +
21A GLY* 3.3 2.8 - - - -
22A GLU* 2.9 31.8 + - + +
24A VAL* 3.2 31.0 - - + -
55A ILE* 3.8 14.6 - - + -
56A GLN* 1.3 76.4 - - - +
58A LYS* 1.3 61.6 + - - +
59A GLU 4.6 2.0 - - - +
62A ASP* 3.6 18.4 - - + +
80A LEU* 4.3 11.4 - - + -
82A LEU* 3.8 16.4 - - + -
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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