Contacts of the strand formed by residues 101 - 106 (chain A) in PDB entry 3O4O
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 PHE 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PRO* 3.1 2.6 - - - +
58A VAL* 2.2 49.4 + - + +
60A LEU* 3.9 21.8 - - + -
69A LEU* 3.8 26.2 - - + -
70A SER* 4.7 1.1 - - - -
71A CYS* 3.9 29.4 - - - -
80A LEU* 4.2 14.6 - - + -
99A PHE 4.1 7.2 - - - -
100A VAL* 1.3 83.5 - - - +
102A ASN* 1.3 54.7 - - - +
103A LYS 4.1 0.4 - - - -
112A PHE* 4.3 18.2 - - + -
113A GLU 3.3 19.7 - - - +
114A SER* 3.8 7.0 - - - -
115A ALA 4.6 1.3 - - - +
122A ILE* 3.9 34.1 - - + -
134A LEU* 4.1 6.5 - - + -
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Residues in contact with ASN 102 (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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50A GLU* 5.8 5.3 - - - +
55A LYS* 3.9 32.8 - - + +
56A ILE 3.2 7.9 - - - +
57A PRO* 3.7 19.7 - - + +
100A VAL* 6.1 0.4 - - - +
101A PHE* 1.3 75.7 - - - +
103A LYS* 1.3 65.6 + - - +
104A ILE* 3.4 9.2 + - - +
112A PHE* 4.7 0.9 - - - -
113A GLU* 2.9 45.7 + - - +
114A SER 4.5 0.3 - - - -
115A ALA* 4.8 15.8 - - - +
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Residues in contact with LYS 103 (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 MET* 4.4 17.2 - - + -
46A PHE* 4.6 6.6 - - - -
54A ASP 3.8 3.3 - - - +
55A LYS* 4.1 0.4 - - - -
56A ILE* 2.9 52.4 + - + +
58A VAL* 4.0 14.6 - - + +
102A ASN* 1.3 70.1 - - - +
104A ILE* 1.3 60.0 + - - +
105A GLU* 3.6 33.6 + - + +
110A LEU* 5.1 3.4 - - + -
111A GLU 3.2 9.0 - - - +
112A PHE* 3.4 27.6 - - + -
148A MET* 4.4 13.5 - - + +
150A PHE* 6.2 1.4 - - - -
256C THR* 3.6 31.1 + - - -
318C THR* 6.0 1.6 - - - -
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Residues in contact with ILE 104 (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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54A ASP* 4.1 12.1 - - - +
55A LYS* 5.1 10.1 - - + -
102A ASN 3.8 10.3 - - - +
103A LYS* 1.3 72.4 - - - +
105A GLU* 1.3 61.1 + - - +
106A ILE* 3.9 9.1 + - + +
109A LYS 3.9 1.2 - - - +
110A LEU* 3.3 2.0 - - - -
111A GLU* 2.9 56.1 + - + +
113A GLU* 4.5 8.7 - - + -
121A TYR* 4.1 21.8 - - + +
184B ILE* 5.4 4.0 - - + -
286B ARG* 3.7 49.4 - - - +
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Residues in contact with GLU 105 (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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54A ASP 4.7 4.4 + - - +
103A LYS* 3.6 27.5 + - + -
104A ILE* 1.3 74.6 - - - +
106A ILE* 1.3 70.7 + - - +
107A ASN 5.8 0.2 + - - -
108A ASN* 4.5 21.2 + - - +
109A LYS 3.6 5.2 - - - +
110A LEU* 3.2 38.9 - - + +
148A MET* 3.8 12.3 - - - +
256C THR* 5.4 2.4 - - - +
318C THR* 3.8 38.5 + - - +
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Residues in contact with ILE 106 (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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104A ILE* 3.9 9.8 + - + +
105A GLU* 1.3 79.7 - - - +
107A ASN* 1.3 78.8 + - + +
108A ASN 3.3 0.4 - - - -
109A LYS* 2.9 26.1 + - - +
131B ILE* 3.7 29.4 - - + -
132B GLU* 4.3 1.4 - - - +
183B LEU* 6.1 0.2 - - - +
184B ILE* 3.7 26.7 - - + -
285B SER* 4.5 12.1 - - - +
286B ARG* 4.9 6.3 - - + -
287B THR* 4.2 15.3 - - - +
318C THR* 5.6 0.2 - - - -
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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