Contacts of the strand formed by residues 103 - 107 (chain A) in PDB entry 1II4
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 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 3.5 4.5 - - - +
72A VAL* 2.9 36.0 + - + +
74A ILE* 3.8 19.3 - - + -
83A LEU* 3.6 48.5 - - + -
84A ALA* 4.0 4.3 - - - -
85A MET* 4.2 17.5 - - + -
91A LEU* 5.3 0.4 - - + -
100A GLU 3.8 15.7 - - - -
101A CYS 3.6 13.2 - - - -
102A PHE* 1.3 82.5 - - - +
104A PHE* 1.3 64.8 + - - +
105A GLU 3.3 1.7 + - - -
115A TYR* 4.0 20.2 - - + -
116A ARG 3.2 7.2 - - - +
117A SER* 3.6 17.7 - - - -
118A ARG* 4.2 0.4 - - - +
125A VAL* 3.7 22.9 - - + -
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG 5.4 0.9 - - - -
70A GLY* 3.3 10.5 - - - +
71A VAL* 3.5 25.1 - - + +
103A PHE* 1.3 70.9 - - - +
105A GLU* 1.3 62.0 + - - +
106A ARG* 3.8 3.8 + - + +
114A THR* 3.2 7.6 + - - +
115A TYR* 3.4 1.6 - - - -
116A ARG* 2.6 84.2 + - + +
117A SER 4.3 0.2 - - - -
118A ARG* 3.7 37.7 - - + -
121A THR* 5.2 3.8 - - + -
331G ASN* 4.9 13.9 - - + -
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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
----------------------------------------------------------
64A LEU* 4.5 7.4 - - - +
70A GLY* 2.8 19.7 + - - +
72A VAL* 4.3 12.6 - - + -
103A PHE 3.3 1.8 + - - -
104A PHE* 1.3 72.3 - - - +
106A ARG* 1.3 64.4 + - - +
107A LEU 5.3 0.4 - - - +
113A ASN* 3.5 15.5 + - - +
114A THR 3.5 4.0 - - - +
115A TYR* 2.4 45.8 + - + +
150A PRO* 5.9 0.3 - - - +
284E ALA* 4.6 7.2 - - + +
285E GLN* 2.7 49.4 + - - +
347E SER* 3.8 19.1 + - - -
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Residues in contact with ARG 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 PHE* 4.9 4.0 - - + +
105A GLU* 1.3 76.9 - - - +
107A LEU* 1.3 66.8 + - - +
108A GLU* 3.4 30.7 + - - +
113A ASN* 3.0 8.6 - - - -
114A THR* 2.9 45.7 + - - +
347E SER* 4.6 16.6 - - - -
273G ASP* 2.8 38.8 + - - +
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Residues in contact with LEU 107 (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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105A GLU* 5.3 0.6 - - - +
106A ARG* 1.3 78.9 + - - +
108A GLU* 1.3 74.2 - - - +
111A ASN* 3.4 20.0 - - - +
112A TYR 3.4 13.2 - - - +
113A ASN* 3.6 7.0 - - - +
251E ARG* 3.4 39.5 - - + +
252E TRP 4.7 0.7 - - - +
253E PRO* 4.0 34.3 - - + -
283E ASP* 4.5 5.8 - - + +
284E ALA* 5.0 14.2 - - + +
347E SER* 4.6 4.4 + - - -
348E ILE* 5.1 10.1 - - + -
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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