Contacts of the strand formed by residues 185 - 191 (chain D) in PDB entry 4UI2
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 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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991A ASP* 5.8 0.9 - - - -
993A THR* 3.4 11.0 - - - -
184D GLU* 1.3 76.3 - - - +
186D ALA* 1.3 60.4 + - - -
187D TRP* 3.4 7.4 - - - -
199D VAL 3.3 2.8 - - - +
200D THR* 3.1 12.8 - - - -
201D ASN 2.9 37.3 + - - -
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Residues in contact with ALA 186 (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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991A ASP* 3.1 29.6 + - + +
993A THR* 2.8 14.1 + - - +
1007A ASN* 2.9 41.1 + - + +
1008A TRP* 3.8 17.0 - - - +
1009A GLN* 4.5 1.3 - - + -
185D GLY* 1.3 69.4 - - - -
187D TRP* 1.3 66.3 + - - +
198D GLN* 4.4 1.6 - - + +
199D VAL 3.3 6.1 - - - +
200D THR* 4.2 4.7 - - - +
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Residues in contact with TRP 187 (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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993A THR* 4.4 2.1 - - + +
995A VAL* 4.0 32.5 - - + -
1007A ASN* 4.2 8.7 - - - -
183D VAL* 3.0 48.7 - - + -
184D GLU 2.9 20.6 + - - -
185D GLY 3.4 8.7 - - - -
186D ALA* 1.3 89.6 + - - +
188D PRO* 1.3 70.2 - - + +
189D LEU 3.6 0.2 + - - -
198D GLN* 3.5 6.9 - - - +
199D VAL* 2.7 49.5 + - + +
201D ASN* 4.4 0.4 - - - +
309D LEU* 4.2 16.4 - - + -
311D LEU* 4.1 23.6 - - + -
317D PRO* 4.1 24.0 - - + -
320D GLU* 3.9 28.0 - - + -
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Residues in contact with PRO 188 (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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1007A ASN* 3.5 22.0 - - - +
1047A THR* 3.8 23.3 - - + -
187D TRP* 1.3 92.0 - - + +
189D LEU* 1.3 63.1 + - - +
190D ILE 4.3 8.5 - - - +
191D ASP* 4.6 2.2 - - + -
197D VAL 3.5 2.2 - - - +
198D GLN* 3.2 21.5 - - - +
309D LEU* 3.3 29.2 - - + +
310D GLN* 3.5 1.6 - - - -
311D LEU* 3.0 24.0 + - - +
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Residues in contact with LEU 189 (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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163C CYS* 5.0 3.1 - - - -
164C GLY 5.3 0.2 - - - -
165C LEU* 4.1 23.3 - - + -
171D LEU* 5.3 2.2 - - + -
187D TRP 4.0 0.2 - - - +
188D PRO* 1.3 77.2 - - - +
190D ILE* 1.3 66.9 + - + +
197D VAL* 3.0 16.7 + - + +
199D VAL* 3.5 33.9 - - + -
291D LEU* 3.1 35.2 - - + -
310D GLN* 3.5 5.0 - - - +
311D LEU* 3.3 30.7 + - + +
312D CYS* 3.0 40.4 + - - +
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Residues in contact with ILE 190 (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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174D PHE* 4.0 23.1 - - + -
188D PRO* 4.3 3.8 - - - +
189D LEU* 1.3 85.3 - - + +
191D ASP* 1.3 68.5 + - - +
192D ASN* 3.1 30.1 - - - +
195D LEU* 3.7 24.7 - - + +
196D SER* 3.4 3.0 - - - -
197D VAL* 2.8 43.6 + - + +
198D GLN* 4.7 0.9 - - - +
293D ILE* 3.6 31.4 - - + -
295D MET* 4.5 2.5 - - - -
310D GLN* 3.9 10.8 - - - +
312D CYS* 3.8 9.9 - - + -
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Residues in contact with ASP 191 (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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1045A ARG* 2.9 52.1 + - - +
1046A LEU 4.4 1.4 + - - -
1047A THR* 3.5 23.8 - - + +
188D PRO* 4.6 4.5 - - + -
190D ILE* 1.3 76.7 - - - +
192D ASN* 1.3 59.3 + - - +
195D LEU 3.7 4.3 - - - -
196D SER* 3.2 15.4 + - - -
198D GLN* 5.7 0.6 - - - +
221D LYS* 4.4 0.4 - - - -
307D GLN* 3.1 22.6 - - + +
309D LEU 4.7 1.1 - - - +
310D GLN* 2.3 32.6 + - + +
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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