Contacts of the strand formed by residues 191 - 198 (chain D) in PDB entry 6D6U
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 TYR 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D VAL* 3.6 32.1 - - + -
55D ASP* 2.7 16.5 + - - -
141D MET* 4.2 0.2 - - - -
151D HIS* 3.4 28.1 + + - -
188D LEU* 3.2 26.6 - - + +
189D ASN 4.1 4.3 - - - +
190D GLN* 1.3 95.7 - - + +
192D ASP* 1.3 62.2 + - - +
219D LEU* 3.7 33.9 - - + -
220D LYS 3.7 7.4 - - - +
221D ARG* 2.5 68.7 + - + -
222D LYS* 4.1 6.1 - - - -
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Residues in contact with ASP 192 (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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188D LEU* 5.0 1.3 - - - -
191D TYR* 1.3 77.2 - - - +
193D LEU* 1.3 81.6 + - - +
194D LEU* 3.3 17.9 - - + +
219D LEU* 3.7 7.9 - - - -
220D LYS* 3.1 25.7 + - + +
222D LYS* 4.7 14.1 - - + +
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Residues in contact with LEU 193 (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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50D PHE* 5.1 19.1 - - + -
181D VAL* 3.8 37.7 - - + -
186D SER* 4.8 19.7 + - - +
188D LEU* 5.7 3.2 - - + +
192D ASP* 1.3 90.8 + - - +
194D LEU* 1.3 68.0 + - - +
195D GLY* 4.3 15.3 - - - +
196D GLN* 4.3 5.4 - - - +
217D PHE* 4.7 16.4 - - + -
218D HIS 3.5 18.6 - - - +
219D LEU* 4.1 12.1 - - + +
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Residues in contact with LEU 194 (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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192D ASP* 3.3 25.1 - - + +
193D LEU* 1.3 83.3 - - - +
195D GLY* 1.3 60.1 + - - +
218D HIS* 3.6 22.4 + - + +
219D LEU 4.8 1.3 - - - -
220D LYS* 4.2 25.1 - - + +
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Residues in contact with GLY 195 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D LEU* 4.3 4.6 - - - +
194D LEU* 1.3 82.8 - - - +
196D GLN* 1.3 82.5 + - - +
217D PHE* 4.0 5.0 - - - -
218D HIS* 3.8 26.0 + - - +
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Residues in contact with GLN 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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176D ALA 5.9 2.2 - - - +
179D VAL* 3.8 34.7 - - + +
180D VAL 5.1 0.4 - - - -
181D VAL* 3.4 38.4 + - - +
193D LEU* 4.3 6.7 - - - +
195D GLY* 1.3 87.0 + - - +
197D THR* 1.3 68.3 + - - +
198D VAL* 5.4 2.0 - - + -
215D THR* 5.1 2.0 - - + -
216D HIS 3.5 6.3 - - - +
217D PHE* 3.8 29.4 - - + -
218D HIS* 4.8 1.5 - - - -
92L TYR* 4.1 8.2 + - - -
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Residues in contact with THR 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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196D GLN* 1.3 80.1 + - - +
198D VAL* 1.3 65.4 + - - +
199D ASP* 5.6 0.7 - - + -
215D THR* 3.3 3.5 - - - +
216D HIS* 2.7 59.2 + - + +
218D HIS* 3.2 20.2 + - + +
28L TYR* 3.4 43.1 - - + +
92L TYR* 4.0 4.8 + - - -
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Residues in contact with VAL 198 (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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171D TRP* 4.0 17.7 - - + +
175D PRO* 3.2 47.8 - - + +
179D VAL* 3.7 32.8 - - + -
196D GLN* 5.4 1.3 - - + -
197D THR* 1.3 84.9 - - - +
199D ASP* 1.3 65.4 + - - +
214D THR 3.4 11.2 - - - +
215D THR* 4.0 4.5 - - + +
28L TYR* 4.5 2.3 + - - -
30L GLY* 4.5 1.9 - - - -
32L TYR* 4.4 3.8 - - - -
92L TYR* 3.7 22.7 + - + +
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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