Contacts of the strand formed by residues 53 - 57 (chain A) in PDB entry 3OEH
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 GLU 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.4 14.4 - - + -
50A GLN* 2.8 48.5 + - + +
51A ALA 3.4 0.8 + - - -
52A GLU* 1.3 78.3 - - - +
54A LEU* 1.3 75.7 - - - +
55A VAL* 3.5 1.0 + - - +
64A MET* 3.4 2.2 - - - -
65A ALA* 3.1 25.9 + - - +
92A ARG* 2.7 47.7 + - - +
93A THR 3.5 0.2 + - - -
94A GLY* 2.9 25.6 + - - +
95A ASN 3.8 14.8 - - - +
96A ILE* 4.2 3.6 - - - +
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Residues in contact with LEU 54 (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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52A GLU 3.7 2.8 + - - -
53A GLU* 1.3 82.0 - - - +
55A VAL* 1.3 63.8 + - - +
62A LYS* 4.2 26.5 - - + +
63A GLY 3.6 4.9 - - - +
64A MET* 4.5 1.1 - - - +
78A PHE* 3.6 26.5 - - + -
93A THR* 2.8 39.8 + - + +
95A ASN* 3.1 16.6 + - + +
97A VAL* 3.5 36.8 - - + +
113A LEU* 4.6 5.8 - - + -
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Residues in contact with VAL 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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46A LEU* 4.5 4.3 - - + -
49A ILE* 3.1 35.9 - - + -
53A GLU 4.2 3.1 - - - +
54A LEU* 1.3 76.6 - - - +
56A GLU* 1.3 62.8 + - - +
57A PHE* 4.0 6.5 - - + -
62A LYS* 3.2 10.6 - - - +
63A GLY 2.6 42.7 + - - +
65A ALA* 5.0 1.1 - - + -
75A ILE* 3.7 38.1 - - + -
90A VAL* 3.8 12.3 - - + -
91A LYS 3.5 14.4 - - - +
92A ARG* 4.6 2.7 - - - -
93A THR* 3.9 4.2 - - - +
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Residues in contact with GLU 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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55A VAL* 1.3 79.4 - - - +
57A PHE* 1.3 73.1 + - - +
60A GLY* 5.4 6.1 - - - +
61A VAL 3.9 5.2 - - - +
62A LYS* 4.4 20.3 - - + +
90A VAL* 3.4 2.8 - - - -
91A LYS* 2.8 60.7 + - + +
93A THR* 4.2 13.4 - - + +
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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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33A VAL* 3.8 14.6 - - + -
41A ALA* 3.6 27.4 - - + -
43A VAL* 4.3 1.3 - - + -
55A VAL* 4.0 8.1 - - + -
56A GLU* 1.3 87.7 - - - +
58A SER* 1.3 66.4 + - - +
59A SER* 3.2 3.6 - - - +
60A GLY* 3.2 10.8 + - - -
61A VAL* 3.0 41.8 + - + +
62A LYS 4.5 5.4 - - - -
75A ILE* 4.0 23.8 - - + -
77A LEU* 3.4 19.7 - - + -
84A VAL* 3.9 20.2 - - + -
88A GLU* 5.0 2.9 - - + +
89A LEU 3.8 4.9 - - - -
90A VAL* 3.6 31.6 - - + -
91A LYS* 6.0 1.7 - - - +
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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