Contacts of the helix formed by residues 189 - 197 (chain A) 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 GLY 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 5.1 3.3 - - - +
187A SER 4.7 0.2 - - - +
188A SER* 1.3 78.9 - - - +
190A ALA* 1.3 66.7 + - - +
191A ALA 3.6 1.1 - - - -
192A ALA* 4.2 2.0 - - - -
193A GLY* 3.1 19.9 + - - -
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Residues in contact with ALA 190 (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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140A VAL* 4.3 9.9 - - - +
141A ALA* 4.7 11.0 - - + +
189A GLY* 1.3 67.6 - - - +
191A ALA* 1.3 68.4 + - - +
193A GLY* 2.9 4.0 + - - -
194A ASN* 2.9 32.7 + - - +
187B SER* 3.9 28.3 - - - +
188B SER 6.1 0.4 - - - +
192B ALA* 5.2 1.8 - - + -
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Residues in contact with ALA 191 (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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189A GLY 3.6 0.2 - - - -
190A ALA* 1.3 78.6 - - - +
192A ALA* 1.3 65.5 + - - +
193A GLY 2.8 1.9 + - - -
194A ASN* 2.8 19.7 + - - +
195A ILE* 3.0 14.6 + - - +
191B ALA* 3.7 16.2 - - + -
192B ALA* 3.6 35.7 - - + +
195B ILE* 4.3 9.6 - - + -
191C ALA* 3.7 8.1 - - + -
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Residues in contact with ALA 192 (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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187A SER* 3.7 24.2 - - - +
188A SER 3.2 26.5 - - - +
189A GLY 3.9 1.0 + - - -
190A ALA 3.4 0.4 - - - -
191A ALA* 1.3 79.3 - - - +
193A GLY* 1.3 58.2 + - - +
195A ILE* 3.7 4.8 + - - +
196A GLN* 2.9 33.8 + - - +
190C ALA* 5.4 0.7 - - + -
191C ALA* 3.4 23.3 - - + +
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Residues in contact with GLY 193 (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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140A VAL* 3.4 17.0 - - - -
187A SER 4.9 1.3 - - - -
189A GLY 3.1 12.5 + - - -
190A ALA 2.9 7.4 + - - -
191A ALA 2.8 2.0 + - - -
192A ALA* 1.3 74.9 - - - +
194A ASN* 1.3 57.9 + - - +
195A ILE 3.1 2.0 - - - -
196A GLN* 3.1 11.9 + - - +
197A THR* 2.8 34.9 + - - -
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Residues in contact with ASN 194 (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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138A TYR 4.0 2.1 - - - +
139A ASP* 3.2 27.1 + - - -
140A VAL* 3.0 27.5 + - - +
178A SER* 5.8 1.6 - - - -
179A LEU* 5.1 1.4 - - - +
182A TYR* 3.5 12.5 - - - -
190A ALA* 2.9 29.2 + - - +
191A ALA* 2.8 13.8 + - - +
193A GLY* 1.3 73.2 - - - -
195A ILE* 1.3 61.1 + - - +
197A THR 3.5 16.2 - - - +
200A GLN* 4.9 0.3 - - - +
183B LEU* 3.9 23.5 - - + +
187B SER* 5.6 1.2 + - - -
192B ALA* 6.2 1.4 - - - +
195B ILE* 4.9 10.6 - - + +
196B GLN* 6.0 1.8 - - - +
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Residues in contact with ILE 195 (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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179A LEU* 4.7 18.8 - - + +
182A TYR* 3.5 12.6 - - - -
183A LEU* 3.1 46.4 + - + -
191A ALA 3.0 12.1 + - - +
192A ALA* 3.8 7.4 - - - +
193A GLY 3.1 0.2 - - - -
194A ASN* 1.3 78.0 - - - +
196A GLN* 1.3 58.9 + - + +
195B ILE* 4.0 15.9 - - + -
178C SER* 6.5 0.2 - - - -
179C LEU* 6.5 0.4 - - + -
191C ALA* 4.0 33.0 - - + +
194C ASN* 4.7 7.4 - - + +
195C ILE* 4.0 24.5 - - + -
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Residues in contact with GLN 196 (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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91A ASN* 3.6 7.5 - - + +
111A TYR* 2.6 29.7 + - - -
182A TYR* 4.3 2.2 - - - -
183A LEU* 3.3 26.2 - - + +
185A GLY* 3.3 30.4 + - - +
186A VAL* 3.4 4.4 + - - +
187A SER* 2.9 45.0 + - - +
192A ALA* 2.9 20.5 + - - +
193A GLY* 3.1 8.1 + - - +
195A ILE* 1.3 84.5 - - + +
197A THR* 1.3 57.4 + - - +
198A PRO* 4.3 0.9 - - - -
139C ASP* 5.1 1.9 - - - +
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Residues in contact with THR 197 (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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89A LEU* 3.7 27.1 - - + +
90A PHE 3.5 8.3 - - - +
91A ASN* 3.2 28.9 + - - +
138A TYR 6.0 0.7 - - - -
140A VAL* 4.6 0.8 - - + +
182A TYR* 4.0 3.9 - - - -
193A GLY 2.8 15.1 + - - +
194A ASN* 3.5 17.0 - - - +
195A ILE 3.6 0.2 - - - -
196A GLN* 1.3 80.3 + - - +
198A PRO* 1.3 64.2 - - - +
199A PHE* 3.1 30.0 - - - +
200A GLN* 4.0 6.0 - - - +
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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