Contacts of the strand formed by residues 191 - 197 (chain A) in PDB entry 1OIZ
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 VAL 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.9 18.6 - - + -
156A ALA* 6.0 0.7 - - + -
182A VAL 4.5 0.2 - - - +
183A LEU* 3.8 28.3 - - + +
189A LEU 3.5 9.0 + - - +
190A LYS* 1.3 69.5 - - - +
192A ARG* 1.3 60.0 + - - +
193A GLY 4.1 9.0 - - - +
194A ILE* 3.7 35.2 - - + -
217A LYS 4.4 5.3 - - - +
218A ILE* 5.8 1.6 - - + -
221A ARG* 3.3 22.0 + - + -
1275A TRT 3.4 32.1 - - + -
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Residues in contact with ARG 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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110A THR* 5.7 5.1 + - - +
112A SER* 4.0 3.4 - - - +
152A ASN 3.6 24.6 + - - +
153A GLY* 4.0 0.7 - - - -
154A ILE 2.9 13.3 + - - +
155A LYS* 3.6 24.4 - - - +
190A LYS* 3.7 27.0 - - - +
191A VAL* 1.3 73.0 - - - +
193A GLY* 1.3 57.4 + - - +
221A ARG* 3.2 61.0 + - - +
223A HIS* 5.3 1.9 - - - -
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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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154A ILE 3.6 3.9 + - - +
155A LYS* 3.3 13.9 - - - +
156A ALA 3.0 24.1 + - - -
191A VAL* 3.4 4.8 + - - +
192A ARG* 1.3 82.0 - - - +
194A ILE* 1.3 67.3 + - - +
195A HIS* 4.1 11.9 - - - -
221A ARG* 3.3 11.2 - - - -
223A HIS* 4.8 2.5 - - - -
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Residues in contact with ILE 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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156A ALA* 3.6 6.7 - - + -
158A PHE* 4.2 25.6 - - + -
183A LEU* 4.1 28.5 - - + -
191A VAL* 3.7 23.3 - - + -
193A GLY* 1.3 77.0 - - - +
195A HIS* 1.3 63.2 + - - +
196A LEU* 4.2 12.7 + - + -
218A ILE* 4.3 15.0 - - + -
221A ARG* 2.7 13.9 + - + +
222A ILE* 3.5 22.0 - - + +
223A HIS* 2.9 27.4 + - - +
1274A TRT 4.5 18.4 - - + -
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Residues in contact with HIS 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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155A LYS* 4.4 8.4 - - + +
156A ALA 2.8 17.6 + - - +
157A ILE* 3.3 12.7 - - + +
158A PHE* 2.7 33.1 + - - +
193A GLY* 4.1 5.5 - - - -
194A ILE* 1.3 83.3 - - - +
196A LEU* 1.3 60.4 + - - +
223A HIS* 3.3 30.4 + + - +
225A HIS* 2.9 28.1 + - + +
233A LEU* 4.3 3.8 - - + +
236A HIS* 3.5 34.7 + + - -
237A PHE* 3.7 30.7 - + - -
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Residues in contact with LEU 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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158A PHE* 3.5 28.7 - - + +
160A LEU* 4.9 5.6 - - + -
194A ILE* 4.3 13.0 - - + +
195A HIS* 1.3 81.1 - - - +
197A ILE* 1.3 58.0 + - - +
199A GLU* 3.4 22.0 - - + +
203A PHE* 3.6 35.0 - - + -
222A ILE* 5.5 0.7 - - + -
223A HIS 2.9 9.4 + - - +
224A MET* 4.0 27.8 - - + -
225A HIS* 2.8 36.6 + - - -
1274A TRT 4.3 9.6 - - + -
1275A TRT 4.9 9.9 - - - -
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Residues in contact with ILE 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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157A ILE* 4.5 10.5 - - + -
158A PHE 3.0 7.9 + - - +
159A ASP* 3.7 23.3 - - + +
160A LEU* 2.9 27.0 + - - +
196A LEU* 1.3 79.0 - - - +
198A ASN* 1.3 63.0 + - - +
199A GLU* 3.0 8.7 + - - -
225A HIS* 3.9 12.8 - - + -
226A GLY 3.8 3.1 - - - -
229A TYR* 3.7 44.2 - - + -
233A LEU* 4.2 17.0 - - + -
245A TYR* 3.6 38.8 - - + -
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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