Contacts of the strand formed by residues 169 - 179 (chain D) in PDB entry 1QD6
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 TRP 169 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D TRP* 3.6 26.2 - + + -
165D GLU* 3.4 7.2 - - - +
166D ASN* 3.0 38.8 + - + +
167D GLY 4.1 2.4 - - - +
168D ASN* 1.3 83.3 - - + +
170D LEU* 1.3 62.9 + - - +
171D VAL* 5.4 0.7 - - + -
199D ILE* 3.7 26.7 - - + -
200D GLY 3.5 15.0 - - - -
201D TYR* 3.3 43.1 - + + -
269D PHE* 4.3 4.1 - - - -
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Residues in contact with LEU 170 (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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15B ARG 4.1 2.2 - - - +
16B GLY* 4.0 15.5 - - - +
163D MET* 4.0 30.7 - - + -
164D ALA 3.5 4.9 - - - -
165D GLU* 4.4 2.7 - - + +
169D TRP* 1.3 76.8 - - - +
171D VAL* 1.3 82.9 + - - +
172D GLU* 4.2 10.1 - - + +
198D LYS* 4.8 1.8 - - + +
199D ILE* 3.4 1.7 - - - +
200D GLY 2.8 33.0 + - - +
268D LEU* 4.3 24.0 - - + +
269D PHE* 3.8 45.1 - - + -
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Residues in contact with VAL 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D TRP* 3.6 31.8 - - + -
162D LEU 3.9 0.9 - - - +
163D MET* 3.5 2.3 - - - +
164D ALA* 2.8 36.3 + - + +
169D TRP* 5.4 1.3 - - + -
170D LEU* 1.3 82.2 - - - +
172D GLU* 1.3 64.3 + - - +
173D VAL* 4.8 6.3 - - + -
197D LEU* 4.0 18.4 - - + -
198D LYS 3.3 7.6 - - - +
199D ILE* 4.4 17.9 - - + -
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Residues in contact with GLU 172 (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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18B ILE* 4.9 4.5 - - - +
161D ARG* 3.0 53.8 + - + +
162D LEU 3.3 8.3 - - - +
163D MET* 4.6 5.5 - - + +
170D LEU* 4.4 8.4 - - + +
171D VAL* 1.3 76.0 - - - +
173D VAL* 1.3 66.0 + - - +
174D LYS* 4.9 5.2 - - - +
196D GLN* 3.7 6.1 + - - +
197D LEU* 3.5 5.2 - - - +
198D LYS* 2.7 85.7 + - + +
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Residues in contact with VAL 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ARG* 3.6 0.7 - - - +
162D LEU* 2.9 58.5 + - + +
171D VAL* 4.3 6.9 - - + -
172D GLU* 1.3 74.8 - - - +
174D LYS* 1.3 59.1 + - - +
175D PRO* 3.5 10.8 - - + +
195D TYR* 6.0 5.2 - - + -
196D GLN 3.6 4.3 - - - +
197D LEU* 3.5 24.9 - - + -
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Residues in contact with LYS 174 (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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35D TYR* 4.2 9.8 + - - -
115D GLU* 4.3 6.5 + - - -
117D GLN* 2.8 30.4 + - - +
141D ASN* 4.1 7.8 - - - +
157D ARG* 5.5 3.8 - - - +
159D TYR* 3.5 34.8 - - + -
160D THR 3.2 10.3 - - - +
161D ARG* 4.4 15.6 - - + +
172D GLU* 4.9 6.5 - - - +
173D VAL* 1.3 74.5 - - - +
175D PRO* 1.3 59.3 - - - +
176D TRP* 3.2 21.5 - - + -
195D TYR* 4.1 1.3 - - - +
196D GLN* 2.8 54.0 + - + +
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Residues in contact with PRO 175 (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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159D TYR* 3.3 5.0 - - - +
160D THR* 3.0 48.9 + - + +
162D LEU* 5.3 5.6 - - + -
173D VAL* 3.5 15.0 - - + +
174D LYS* 1.3 86.8 - - - +
176D TRP* 1.3 60.7 + - - +
194D TYR 3.4 9.6 - - - +
195D TYR* 3.8 9.4 - - + -
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Residues in contact with TRP 176 (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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155D TRP* 3.7 23.5 - + - -
157D ARG* 3.4 42.8 - - + -
158D LEU 3.2 12.6 - - - +
159D TYR* 3.9 7.6 - - + -
174D LYS* 3.2 30.7 - - + -
175D PRO* 1.3 76.4 - - - +
177D TYR* 1.3 62.1 + - - +
178D VAL* 4.4 9.4 - - + +
192D MET 3.6 10.8 - - - -
193D GLY 3.0 27.5 + - - -
194D TYR* 2.8 33.6 + + + +
195D TYR 3.5 17.7 - - - -
196D GLN* 3.5 29.2 - - + -
213D GLN* 3.8 15.5 - - - -
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Residues in contact with TYR 177 (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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157D ARG* 3.3 2.9 - - - -
158D LEU* 2.7 49.6 + - + +
176D TRP* 1.3 74.8 - - - +
178D VAL* 1.3 80.0 + - - +
179D VAL* 3.4 30.4 + - + +
194D TYR* 5.8 1.3 - + - -
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Residues in contact with VAL 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D TRP* 3.6 25.4 - - + -
156D ASN 3.3 13.0 - - - +
157D ARG* 4.2 3.6 - - + -
176D TRP* 4.4 5.2 - - + -
177D TYR* 1.3 89.0 - - - +
179D VAL* 1.3 68.3 + - - +
180D GLY 5.0 1.3 - - - +
182D THR* 3.7 30.3 - - + -
188D ILE* 5.7 0.4 - - + -
189D THR* 3.4 33.0 - - + -
194D TYR* 5.3 4.7 - - + -
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Residues in contact with VAL 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TYR* 4.8 6.5 - - + -
156D ASN* 3.0 46.0 + - + +
157D ARG 4.5 1.3 - - - +
158D LEU* 3.9 31.9 - - + +
177D TYR* 3.4 37.7 + - + +
178D VAL* 1.3 76.2 - - - +
180D GLY* 1.3 69.3 + - - +
181D ASN 4.5 0.9 - - - +
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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