Contacts of the strand formed by residues 121 - 127 (chain C) in PDB entry 1A6Z
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 GLN 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C GLY* 3.2 1.9 - - - -
118C TYR 2.9 30.3 + - - +
119C ASP* 3.3 15.9 - - + +
120C GLY* 1.3 80.5 + - - +
122C ASP* 1.3 73.7 + - - +
123C HIS* 4.0 0.2 - - - +
137C GLU* 5.1 5.4 - - - +
1D ILE* 3.8 30.0 + - + +
60D TRP* 3.7 5.2 - - - -
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Residues in contact with ASP 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C LYS* 5.0 14.2 - - - +
116C TYR 4.1 2.5 - - - -
121C GLN* 1.3 78.1 - - - +
123C HIS* 1.3 59.4 + - - +
136C ALA* 3.8 21.3 - - + +
137C GLU* 3.6 14.6 - - - +
58D LYS 4.8 3.1 - - - +
59D ASP* 5.9 0.3 - - - -
60D TRP* 2.7 37.1 + - - +
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Residues in contact with HIS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ILE* 3.9 23.8 - - + +
87C HIS* 3.1 37.7 + + - -
116C TYR* 2.9 17.7 + - + +
118C TYR* 3.8 26.3 - - + +
122C ASP* 1.3 77.5 - - - +
124C LEU* 1.3 89.4 + - + +
136C ALA* 2.8 30.0 + - - +
137C GLU* 3.7 15.1 + - - -
139C ARG 4.1 0.4 + - - -
140C ALA* 3.3 41.7 - - + +
143C THR* 4.7 2.6 + - - -
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ILE* 4.6 2.9 - - + -
115C LYS* 3.7 1.4 - - - +
116C TYR* 2.7 47.7 + - + +
123C HIS* 1.3 104.8 - - + +
125C GLU* 1.3 60.5 + - - +
133C TRP* 4.3 9.4 - - + -
134C ARG 3.4 14.6 - - - +
135C ALA* 3.9 7.6 - - - -
136C ALA* 5.9 0.4 - - - -
140C ALA* 3.8 16.6 - - + +
143C THR* 3.3 35.7 - - + -
144C LYS* 4.0 15.9 - - + -
147C TRP* 3.8 17.7 - - + -
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C TYR* 5.6 3.5 - - + +
114C TRP 3.7 4.3 - - - +
115C LYS* 3.2 47.4 + - + +
124C LEU* 1.3 77.7 - - - +
126C PHE* 1.3 75.1 + - - +
127C CYS* 3.5 7.5 + - - -
133C TRP* 3.3 5.1 - - - -
134C ARG* 2.7 69.5 + - - +
136C ALA* 6.5 0.7 - - + -
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Residues in contact with PHE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C TYR* 5.2 2.1 - - - +
114C TRP* 2.8 37.6 + - + +
116C TYR* 5.6 0.2 - - - -
125C GLU* 1.3 84.2 - - - +
127C CYS* 1.3 61.0 + - - +
128C PRO* 3.4 32.6 - - + +
131C LEU* 4.7 1.8 - - + -
132C ASP 3.2 23.3 - - - -
133C TRP* 3.4 39.9 - + - +
154C ALA* 3.5 34.1 - - + -
157C ASN* 3.7 11.9 - - + -
158C ARG* 3.6 26.5 - - + -
161C LEU* 3.7 20.6 - - + -
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Residues in contact with CYS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU* 3.7 20.6 - - - -
126C PHE* 1.3 75.3 - - - +
128C PRO* 1.3 69.2 - - - +
129C ASP* 3.3 2.9 - - + -
130C THR* 3.4 18.5 + - - +
131C LEU 3.1 16.5 + - - -
132C ASP* 2.9 22.9 + - - +
133C TRP 4.7 0.2 - - - -
134C ARG* 3.9 31.4 - - - -
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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