Contacts of the strand formed by residues 154 - 166 (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 SER 154 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D HIS* 4.2 12.3 - - - -
143D ASP 3.2 14.1 - - - -
144D SER* 3.8 13.2 - - - -
152D SER* 5.5 0.9 - - - -
153D ARG* 1.3 75.9 - - - +
155D TRP* 1.3 63.7 + - - +
156D ASN* 5.4 1.2 + - - -
181D ASN* 4.7 5.6 + - - +
182D THR* 4.2 11.1 - - - -
184D ASP* 3.5 17.0 + - - +
185D ASN* 2.8 29.7 + - - +
249D LEU* 4.5 3.2 - - - +
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Residues in contact with TRP 155 (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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141D ASN* 4.1 0.5 - - - +
142D HIS* 3.4 5.2 + - - -
143D ASP* 3.1 65.2 + - + +
154D SER* 1.3 77.5 - - - +
156D ASN* 1.3 68.9 + - - +
157D ARG* 3.5 41.2 + - + +
176D TRP* 3.7 15.7 - + - -
178D VAL* 3.6 33.0 - - + -
181D ASN 4.8 0.4 - - - -
182D THR* 4.0 18.2 - - + -
185D ASN* 4.3 3.4 - - - +
188D ILE* 3.7 31.6 - - + +
189D THR* 4.2 9.9 - - + -
192D MET* 3.5 41.7 - - + -
249D LEU* 4.1 4.9 - - + +
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Residues in contact with ASN 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TYR* 2.5 36.9 + - + -
141D ASN 3.4 4.5 - - - -
142D HIS* 3.0 21.6 + - - -
154D SER* 5.4 1.6 + - - -
155D TRP* 1.3 79.7 - - - +
157D ARG* 1.3 64.0 + - - +
178D VAL* 3.3 9.2 - - - +
179D VAL* 3.0 44.5 + - + +
180D GLY* 5.0 1.9 - - - -
181D ASN* 3.9 22.4 + - - +
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Residues in contact with ARG 157 (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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115D GLU* 3.7 11.1 + - - -
140D TYR* 3.5 5.4 - - - -
141D ASN* 2.8 74.7 + - + +
143D ASP* 3.7 22.0 + - - +
155D TRP* 3.5 44.1 - - + +
156D ASN* 1.3 80.2 - - - +
158D LEU* 1.3 63.5 + - - +
159D TYR* 4.0 1.5 + - + -
174D LYS* 5.5 4.4 - - - +
176D TRP* 3.4 65.9 - - + -
177D TYR 3.3 5.2 - - - +
178D VAL* 4.2 4.9 - - + -
179D VAL* 4.5 1.3 - - - +
192D MET* 5.5 2.0 - - - +
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Residues in contact with LEU 158 (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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138D MET* 5.4 9.4 - - + -
139D GLY 3.4 11.4 - - - +
140D TYR* 4.2 24.9 - - + -
157D ARG* 1.3 72.6 - - - +
159D TYR* 1.3 58.5 + - - +
176D TRP* 3.2 1.8 - - - -
177D TYR* 2.7 51.3 + - + +
179D VAL* 3.9 29.8 - - + -
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Residues in contact with TYR 159 (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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117D GLN* 3.2 30.3 + - - +
119D PHE* 3.4 16.2 - - + +
137D GLU* 2.7 35.6 + - + -
138D MET* 3.4 10.4 - - - +
139D GLY 3.0 56.6 + - - -
140D TYR 3.7 9.0 - - - -
141D ASN* 3.9 16.8 - - + -
157D ARG* 5.2 1.1 - - + -
158D LEU* 1.3 75.5 - - - +
160D THR* 1.3 74.6 + - - +
161D ARG* 3.8 8.3 - - + -
174D LYS* 3.5 28.3 - - + -
175D PRO 3.3 14.6 - - - +
176D TRP* 3.9 10.1 - - + +
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Residues in contact with THR 160 (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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136D VAL* 5.0 3.6 - - + -
137D GLU 3.1 17.3 - - - +
138D MET* 4.1 18.2 - - + +
159D TYR* 1.3 79.7 + - - +
161D ARG* 1.3 60.1 + - - +
162D LEU* 3.6 32.8 - - + -
174D LYS* 3.2 6.8 - - - +
175D PRO* 3.0 40.5 + - - +
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Residues in contact with ARG 161 (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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16B GLY 5.4 1.2 + - - -
18B ILE* 3.8 26.7 - - - +
19B ILE* 3.9 4.9 - - - +
35D TYR* 3.7 17.7 + - - -
135D ASP* 3.0 34.4 + - - +
136D VAL* 3.6 3.3 - - - -
137D GLU* 2.7 71.4 + - + +
159D TYR* 3.8 13.3 - - + -
160D THR* 1.3 73.7 - - - +
162D LEU* 1.3 62.9 + - - +
163D MET* 3.7 22.2 - - - +
172D GLU* 3.0 45.8 + - + +
173D VAL 3.6 3.4 - - - +
174D LYS* 4.3 11.7 - - + +
198D LYS* 5.7 0.2 - - - +
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Residues in contact with LEU 162 (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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133D LEU* 4.3 14.1 - - + -
135D ASP 3.4 3.4 - - - +
136D VAL* 3.8 28.9 - - + -
160D THR* 3.6 27.1 - - + -
161D ARG* 1.3 76.7 - - - +
163D MET* 1.3 59.8 + - - +
171D VAL 3.9 1.0 - - - +
172D GLU* 3.3 5.8 - - - +
173D VAL* 2.9 55.4 + - + +
175D PRO* 5.3 5.8 - - + -
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Residues in contact with MET 163 (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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14B VAL* 5.1 0.4 - - + -
15B ARG 4.6 3.4 - - - +
16B GLY* 3.6 9.0 - - - +
17B SER* 3.5 30.5 - - - +
133D LEU* 3.5 5.5 - - - +
134D ARG* 2.7 47.2 + - + -
135D ASP* 3.0 36.6 + - + +
161D ARG* 3.7 22.4 - - - +
162D LEU* 1.3 74.0 - - - +
164D ALA* 1.3 72.6 + - - +
165D GLU* 4.3 4.7 - - - +
170D LEU* 4.0 32.3 - - + -
171D VAL 3.5 2.9 - - - +
172D GLU* 4.6 4.9 - - + +
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Residues in contact with ALA 164 (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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131D TRP* 3.9 22.5 - - + -
132D THR 3.3 13.9 - - - +
133D LEU* 4.0 16.2 - - + +
162D LEU 4.3 0.4 - - - -
163D MET* 1.3 80.0 - - - +
165D GLU* 1.3 60.1 + - - +
170D LEU* 3.5 2.4 - - - -
171D VAL* 2.8 36.7 + - + +
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Residues in contact with GLU 165 (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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14B VAL* 4.5 7.0 - - - +
15B ARG* 4.0 19.8 + - - +
130D GLY 3.9 0.5 - - - +
131D TRP* 3.3 6.5 - - - -
132D THR* 2.9 43.7 + - - +
134D ARG* 3.0 41.0 + - + +
163D MET* 4.7 6.5 - - - +
164D ALA* 1.3 73.2 - - - +
166D ASN* 1.3 64.9 + - - +
167D GLY 5.4 2.9 - - - +
169D TRP 3.4 12.3 - - - +
170D LEU* 4.9 3.4 - - + -
269D PHE* 6.3 1.1 - - + -
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Residues in contact with ASN 166 (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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129D ALA 5.0 1.0 + - - -
130D GLY* 3.4 23.7 + - - +
131D TRP* 3.6 41.4 - - + +
165D GLU* 1.3 80.3 - - - +
167D GLY* 1.3 68.4 + - - +
168D ASN 3.1 1.0 + - - -
169D TRP* 3.0 31.2 + - - +
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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