Contacts of the strand formed by residues 194 - 197 (chain D) in PDB entry 3IRR
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 LEU 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155D ALA* 3.7 19.1 - - + +
156D THR* 3.3 14.4 - - - +
157D THR* 3.6 25.8 - - + -
186D GLN 3.9 0.2 - - - +
187D LYS* 3.7 3.3 - - - +
188D GLU* 2.8 56.7 + - + +
189D ALA 4.8 9.9 - - - +
190D GLY* 5.5 2.0 - - - -
192D PRO 4.2 5.6 - - - +
193D PRO* 1.3 73.4 - - - +
195D TRP* 1.3 62.5 + - - +
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Residues in contact with TRP 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 3.8 15.6 - - + +
155D ALA* 3.1 5.5 - - - -
156D THR* 2.8 40.2 + - + +
157D THR* 4.6 0.4 - - - -
158D ALA* 4.5 9.3 - - - +
161D LEU* 5.8 0.2 - - + -
173D ASN* 4.8 2.8 + - - -
176D LEU* 3.7 56.3 - - + +
177D TYR* 3.5 43.7 - + - -
180D ALA* 4.3 13.2 - - + -
185D LEU* 4.5 11.2 - - + -
186D GLN 3.7 10.8 - - - -
187D LYS* 3.4 49.4 - - + -
193D PRO* 3.9 20.6 + - - +
194D LEU* 1.3 78.8 - - - +
196D LYS* 1.3 59.6 + - - +
10F C 4.9 2.3 + - - -
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Residues in contact with LYS 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 4.4 6.1 - - - -
153D GLY* 3.0 32.7 + - - +
154D LYS 3.3 17.0 - - - +
155D ALA* 3.7 13.2 - - - +
185D LEU* 3.4 11.7 - - - +
186D GLN* 3.0 48.6 + - + +
188D GLU* 2.9 40.6 + - + +
195D TRP* 1.3 73.3 - - - +
197D ILE* 1.3 68.4 + - - +
199D VAL* 6.3 1.6 - - + -
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Residues in contact with ILE 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU* 5.1 7.0 - - + +
147D LEU* 3.8 21.5 - - + +
148D GLU* 3.4 48.2 - - + +
151D GLY 5.0 0.2 - - - +
152D GLU* 4.1 22.2 - - - +
154D LYS 5.0 0.4 + - - -
184D LYS 4.1 6.1 - - - +
185D LEU* 3.8 9.2 - - + -
186D GLN* 4.4 1.7 - - - +
196D LYS* 1.3 83.8 - - - +
198D ALA* 1.3 76.4 + - - +
199D VAL* 3.6 11.9 + - + +
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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