Contacts of the strand formed by residues 200 - 207 (chain C) in PDB entry 2IZW
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 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C THR* 4.7 9.9 - - - +
88C VAL 3.0 15.7 - - - +
89C LEU* 3.4 28.3 - - + -
136C MET* 3.6 4.9 - - - -
137C LEU* 2.8 53.6 + - + +
138C TYR 3.8 1.6 - - - -
139C ASP 3.1 40.4 + - - +
140C VAL* 3.4 16.2 + - - -
142C ASP 4.9 1.6 + - - -
194C ASN* 4.3 2.1 - - - +
197C THR* 3.9 8.8 - - - +
199C PHE* 1.3 90.8 + - - +
201C ILE* 1.3 67.3 + - - +
202C ALA 3.9 0.2 - - - -
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Residues in contact with ILE 201 (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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71C LEU* 4.2 14.4 - - + -
86C GLY 3.8 0.2 - - - +
87C THR* 3.0 6.8 - - - -
88C VAL* 2.9 42.1 + - + +
90C PHE* 5.5 2.5 - - + -
118C PHE* 3.4 38.4 - - + -
134C MET* 4.7 8.7 - - + -
135C ALA 3.8 1.6 - - - -
136C MET* 4.1 9.9 - - + -
170C LEU* 4.1 14.8 - - + -
199C PHE* 3.3 31.0 - - + -
200C GLN* 1.3 74.6 - - - +
202C ALA* 1.3 70.8 + - - +
203C TRP* 3.9 9.8 - - + -
217C ILE* 5.2 5.2 - - + -
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Residues in contact with ALA 202 (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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86C GLY 3.5 6.3 - - - -
87C THR* 4.0 7.6 - - + -
134C MET* 3.2 4.9 - - - +
135C ALA 3.0 30.9 + - - +
137C LEU* 3.6 31.6 - - + +
146C ILE* 4.3 4.9 - - + -
151C LEU* 3.6 24.9 - - + -
200C GLN 3.9 2.0 + - - -
201C ILE* 1.3 74.4 - - - +
203C TRP* 1.3 64.2 + - - +
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Residues in contact with TRP 203 (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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72C VAL* 4.1 30.2 - - + +
73C ARG 5.7 0.4 - - - -
74C VAL* 3.6 37.0 - - + -
75C THR 5.5 0.7 - - - -
84C VAL* 3.7 20.4 - - + -
85C SER* 3.2 38.4 - - - -
86C GLY* 3.0 48.2 + - - +
87C THR* 3.9 2.2 - - - +
88C VAL* 4.6 4.4 - - + +
132C VAL* 6.0 3.4 - - + -
133C ALA 3.3 12.3 - - - +
134C MET* 4.0 8.5 - - + -
146C ILE* 3.7 1.8 - - - +
151C LEU* 3.4 5.3 - - - +
201C ILE* 3.9 12.8 - - + -
202C ALA* 1.3 76.6 - - - +
204C ALA* 1.3 69.5 + - - +
205C ALA* 4.4 2.2 - - + -
217C ILE* 4.0 21.8 - - + -
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Residues in contact with ALA 204 (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 GLU* 4.0 4.5 - - - +
84C VAL 3.2 13.0 - - - +
85C SER* 3.9 9.2 - - - -
132C VAL* 3.6 1.4 - - - +
133C ALA 2.9 30.8 + - - +
146C ILE* 4.2 0.4 - - + -
147C THR* 3.9 7.6 - - - -
148C ILE* 3.7 33.8 - - + +
151C LEU* 3.6 5.8 - - + +
203C TRP* 1.3 81.4 - - - +
205C ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 205 (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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74C VAL* 4.2 25.6 - - + -
83C GLU* 3.3 6.1 - - - -
84C VAL* 2.7 39.1 + - + +
131C GLU 3.4 13.2 - - - +
132C VAL* 4.1 13.0 - - + -
148C ILE* 3.9 3.1 - - - -
162C ILE* 4.4 7.4 - - + -
203C TRP* 4.3 1.5 - - + -
204C ALA* 1.3 76.7 - - - +
206C GLN* 1.3 60.5 + - - +
214C LEU* 4.5 4.7 - - + -
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Residues in contact with GLN 206 (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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76C SER* 6.4 0.4 - - - +
77C SER 6.3 0.2 - - - +
81C GLY* 3.7 25.6 - - - +
82C THR 3.9 7.0 - - - +
83C GLU* 3.7 15.0 - - + +
84C VAL* 5.6 0.9 - - - -
130C GLY* 3.2 36.6 - - - +
131C GLU* 3.2 25.6 + - + +
148C ILE* 4.1 15.3 - - + -
162C ILE* 4.8 0.7 - - - +
205C ALA* 1.3 77.4 - - - +
207C SER* 1.3 92.0 + - - +
208C SER 4.2 0.5 + - - -
214C LEU* 4.5 5.5 - - - +
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Residues in contact with SER 207 (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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76C SER* 4.0 8.6 + - - +
77C SER* 5.9 0.7 - - - +
81C GLY* 2.8 21.5 + - - -
82C THR 4.5 2.1 + - - +
128C THR* 3.9 2.1 + - - -
129C ASN 2.9 16.9 + - - -
130C GLY* 4.5 0.7 - - - -
162C ILE* 5.1 2.1 - - - +
206C GLN* 1.3 89.3 + - - +
208C SER* 1.3 65.4 + - - +
209C LEU* 3.0 30.6 + - - +
214C LEU* 3.8 28.8 - - - +
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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