Contacts of the strand formed by residues 55 - 59 (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 ARG 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 4.1 0.2 + - - -
46A VAL* 3.9 18.8 - - + -
47A ILE 3.4 2.7 - - - -
48A GLU* 3.1 30.6 + - + +
54A SER* 1.3 88.4 + - - +
56A LYS* 1.3 62.9 + - - +
57A PHE* 4.1 22.9 - - + -
335A LEU 4.7 2.4 + - - -
336A THR* 4.1 13.5 - - - +
337A ASP 5.3 0.4 - - - +
338A TYR* 3.4 34.5 + - - -
72B LYS* 5.7 2.2 - - - +
91B ASP* 3.3 26.0 - - - +
98B LYS* 5.7 1.6 - - - +
160B GLU* 3.5 42.9 + - - +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.5 14.0 - - - +
46A VAL* 3.5 2.9 - - - +
47A ILE* 2.8 45.6 + - + +
49A ASN* 5.9 5.8 - - - +
54A SER 5.6 1.1 - - - +
55A ARG* 1.3 77.2 - - - +
57A PHE* 1.3 77.4 + - - +
92A LEU* 2.7 37.9 + - - +
93A LYS* 4.4 4.6 + - - +
95A LEU* 3.5 22.0 - - + -
91B ASP* 4.5 5.4 - - - +
94B THR* 4.0 23.6 - - + +
96B SER* 3.4 12.1 - - - +
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Residues in contact with PHE 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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44A THR* 4.3 7.4 - - + -
45A ILE 3.4 4.3 - - - +
46A VAL* 4.1 27.1 - - + +
47A ILE* 5.0 0.4 - - - +
55A ARG* 4.1 29.2 - - + -
56A LYS* 1.3 88.3 - - - +
58A ILE* 1.3 64.7 + - - +
59A GLU 4.0 0.7 + - - -
95A LEU* 3.5 6.2 - - - +
338A TYR* 5.7 0.7 - - - -
72B LYS* 6.2 3.6 - - + -
89B VAL* 4.3 12.6 - - + -
90B ALA 4.9 0.7 - - - -
91B ASP* 4.4 9.2 - - + -
96B SER* 2.8 46.9 + - - +
97B ALA 3.8 20.3 + - - +
98B LYS* 3.5 48.2 - - + -
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Residues in contact with ILE 58 (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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44A THR* 3.8 1.5 - - - -
45A ILE* 2.9 44.9 + - + +
47A ILE* 3.9 23.8 - - + -
57A PHE* 1.3 76.2 - - - +
59A GLU* 1.3 63.0 + - - +
61A ALA* 3.9 16.8 - - + +
73A ILE* 3.9 23.8 - - + -
75A PHE* 3.7 46.9 - - + -
77A ARG* 3.9 7.6 - - - +
90A ALA* 4.7 0.9 - - + -
95A LEU* 4.0 16.8 - - + +
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Residues in contact with GLU 59 (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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43A ASN 3.4 1.6 - - - +
44A THR* 2.5 30.4 + - - -
57A PHE 4.0 2.0 + - - -
58A ILE* 1.3 75.0 - - - +
60A ASP* 1.3 92.2 + - + +
61A ALA* 3.3 0.9 + - - +
77A ARG* 3.3 21.6 + - - +
88B TRP* 4.5 15.0 - - + -
97B ALA 3.7 15.9 + - - +
98B LYS* 3.5 7.0 - - - +
99B LYS* 3.0 37.2 + - + +
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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