Contacts of the strand formed by residues 131 - 144 (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 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D TYR 3.6 2.1 - - - +
127D ARG* 4.6 0.2 - - - -
128D PHE* 2.9 40.0 + - + +
129D ALA* 3.1 27.4 + - + -
130D GLY* 1.3 78.2 - - - +
132D THR* 1.3 60.3 + - - +
133D LEU 3.7 0.9 + - - -
164D ALA* 3.9 20.6 - - + -
165D GLU* 3.3 32.3 - - - -
166D ASN* 3.6 27.2 - - + +
169D TRP* 3.6 30.1 - + + -
171D VAL* 3.6 32.3 - - + -
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Residues in contact with THR 132 (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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125D ASP* 3.8 17.3 - - - +
126D TYR 3.3 9.6 - - - +
127D ARG* 3.6 25.9 + - + +
130D GLY 3.8 3.8 + - - -
131D TRP* 1.3 69.5 - - - +
133D LEU* 1.3 71.8 + - - +
134D ARG* 3.2 34.8 + - - +
164D ALA* 4.1 1.3 - - - -
165D GLU* 2.9 46.8 + - - +
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Residues in contact with LEU 133 (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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124D THR* 2.8 32.7 + - + +
125D ASP* 3.7 1.2 - - - -
126D TYR* 2.7 44.4 + - + +
131D TRP 3.7 3.2 + - - -
132D THR* 1.3 69.7 - - - +
134D ARG* 1.3 58.3 + - - +
135D ASP 4.1 7.2 - - - +
136D VAL* 3.6 24.2 - - + -
162D LEU* 4.3 16.2 - - + -
163D MET 3.5 24.2 - - - +
164D ALA* 4.0 10.5 - - + +
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Residues in contact with ARG 134 (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* 4.3 16.7 - - + +
17B SER* 4.3 4.2 + - - -
123D ALA* 3.4 7.4 - - - +
124D THR* 2.9 37.5 + - - +
125D ASP* 3.1 35.8 + - - -
127D ARG* 4.3 6.5 - - - +
132D THR* 3.2 29.4 + - - +
133D LEU* 1.3 71.4 - - - +
135D ASP* 1.3 70.8 + - - +
163D MET* 2.7 27.0 + - + +
165D GLU* 3.0 37.0 + - + +
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Residues in contact with ASP 135 (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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17B SER* 2.6 32.2 + - - -
18B ILE 3.2 5.1 + - - -
19B ILE* 2.9 33.4 + - + +
122D PHE 3.6 3.4 - - - -
133D LEU* 4.1 1.9 - - - +
134D ARG* 1.3 83.3 - - - +
136D VAL* 1.3 66.9 + - - +
137D GLU 4.2 0.2 - - - -
161D ARG* 3.0 29.6 + - - +
162D LEU* 3.4 5.2 - - - -
163D MET* 3.0 45.0 + - + +
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Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 5.3 0.2 - - - -
121D GLY* 3.4 1.6 - - - -
122D PHE* 2.7 56.0 + - + +
124D THR* 4.2 15.7 - - + -
133D LEU* 3.6 27.1 - - + -
135D ASP* 1.3 80.1 - - - +
137D GLU* 1.3 64.2 + - - +
138D MET* 6.1 1.3 - - + -
160D THR* 5.0 3.4 - - + -
161D ARG 3.6 3.1 - - - -
162D LEU* 3.8 17.9 - - + -
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Residues in contact with GLU 137 (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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19B ILE* 4.0 7.1 - - + +
35D TYR* 2.7 27.1 + - - -
119D PHE* 3.5 33.8 - - + -
120D LEU 3.4 4.5 - - - +
121D GLY* 4.6 3.6 - - - -
136D VAL* 1.3 78.5 - - - +
138D MET* 1.3 62.6 + - - +
159D TYR* 2.7 29.4 + - + +
160D THR* 3.1 8.6 - - - +
161D ARG* 2.7 78.1 + - + +
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Residues in contact with MET 138 (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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119D PHE* 3.2 3.5 - - - -
120D LEU* 2.8 40.6 + - + +
122D PHE* 6.5 0.4 - - + -
136D VAL* 5.5 2.2 - - + +
137D GLU* 1.3 74.4 - - - +
139D GLY* 1.3 67.4 + - - +
158D LEU* 5.4 8.1 - - + -
159D TYR* 3.4 26.9 - - - +
160D THR* 4.1 14.4 - - + +
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Residues in contact with GLY 139 (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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118D LEU 3.1 12.3 - - - -
119D PHE* 3.9 1.6 - - - -
138D MET* 1.3 83.3 - - - +
140D TYR* 1.3 58.1 + - - -
158D LEU* 3.4 9.1 - - - +
159D TYR* 3.0 46.1 + - - +
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Residues in contact with TYR 140 (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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116D PRO* 5.5 2.2 - - + -
117D GLN* 3.3 6.9 - - - +
118D LEU* 2.8 44.3 + - + +
139D GLY* 1.3 74.9 - - - -
141D ASN* 1.3 73.6 + - - +
142D HIS* 3.7 21.4 + - + +
156D ASN* 2.5 38.9 + - + -
157D ARG 3.5 8.7 - - - -
158D LEU* 4.2 18.8 - - + -
159D TYR* 3.9 1.3 - - - -
179D VAL* 4.8 5.4 - - + -
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Residues in contact with ASN 141 (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* 2.8 30.6 + - - +
116D PRO 3.7 3.6 - - - -
117D GLN* 2.8 32.2 + - - +
140D TYR* 1.3 80.8 - - - +
142D HIS* 1.3 72.6 + - - +
143D ASP 3.7 0.5 + - - -
156D ASN* 3.4 3.8 - - - -
157D ARG* 2.8 73.0 + - + +
159D TYR* 3.9 9.2 - - + -
174D LYS* 4.1 4.6 - - - +
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Residues in contact with HIS 142 (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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98C TRP* 5.5 2.9 - + - -
115D GLU* 3.3 7.3 - - - -
116D PRO* 3.1 40.5 + - + +
140D TYR* 3.7 18.5 - - + +
141D ASN* 1.3 79.9 - - - +
143D ASP* 1.3 58.0 + - - +
144D SER* 3.6 5.6 - - - -
154D SER* 4.2 18.6 - - - -
155D TRP 3.4 12.1 + - - -
156D ASN* 3.0 29.3 + - - -
270D HDS 3.0 40.2 + - + -
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Residues in contact with ASP 143 (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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113D ASN* 3.9 16.2 - - - +
114D TYR 3.6 6.9 - - - +
115D GLU* 4.0 19.9 - - + +
141D ASN* 3.8 1.1 - - - +
142D HIS* 1.3 75.8 - - - +
144D SER* 1.3 62.1 + - - +
154D SER* 3.2 4.2 - - - -
155D TRP* 3.1 51.3 + - + +
157D ARG* 3.7 21.8 + - - +
192D MET* 5.3 4.2 - - - +
249D LEU* 3.5 25.7 - - - +
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Residues in contact with SER 144 (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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113D ASN* 3.4 4.2 - - - -
114D TYR* 2.8 33.1 + - - -
142D HIS* 3.6 9.4 - - - -
143D ASP* 1.3 76.1 - - - +
145D ASN* 1.3 57.8 + - - +
153D ARG 3.5 6.1 - - - -
154D SER* 3.8 11.4 - - - -
249D LEU* 3.5 5.4 - - - +
270D HDS 1.4 59.7 + - - -
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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