Contacts of the strand formed by residues 154 - 166 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C HIS* 4.1 11.4 - - - -
143C ASP 3.1 9.0 - - - -
144C SER* 3.6 17.9 - - - -
152C SER* 5.5 0.2 - - - -
153C ARG* 1.3 76.8 - - - +
155C TRP* 1.3 64.2 + - - +
156C ASN* 5.7 0.9 + - - -
181C ASN 4.8 2.3 + - - +
182C THR* 4.4 9.5 - - - -
184C ASP* 3.4 18.9 + - - +
185C ASN* 3.0 24.8 + - - +
249C LEU* 4.5 2.6 - - - +
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Residues in contact with TRP 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C ASN* 4.1 0.9 - - - +
142C HIS* 3.7 4.3 + - - -
143C ASP* 2.9 63.5 + - + +
154C SER* 1.3 78.1 - - - +
156C ASN* 1.3 67.3 + - - +
157C ARG* 3.4 44.8 - - + +
176C TRP* 3.7 15.3 - + - -
178C VAL* 3.6 29.6 - - + -
181C ASN 4.9 1.3 - - - -
182C THR* 4.2 17.5 - - + -
185C ASN* 4.3 4.5 - - - +
188C ILE* 3.6 32.9 - - + +
189C THR* 4.1 9.4 - - + -
192C MET* 3.6 41.1 - - + -
249C LEU* 3.9 5.7 - - + +
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Residues in contact with ASN 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C TYR* 2.6 31.8 + - + -
141C ASN 3.3 3.8 - - - -
142C HIS* 2.8 25.6 + - - -
154C SER* 5.6 1.2 + - - -
155C TRP* 1.3 78.6 - - - +
157C ARG* 1.3 69.0 + - - +
178C VAL* 3.4 5.8 - - - +
179C VAL* 3.0 51.3 + - + +
180C GLY* 5.2 1.4 - - - -
181C ASN 4.1 15.8 + - - +
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Residues in contact with ARG 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C GLU* 3.5 16.6 + - - -
140C TYR* 3.5 6.0 - - - -
141C ASN* 2.8 71.2 + - + +
143C ASP* 3.8 20.2 + - - +
155C TRP* 3.4 47.7 + - + +
156C ASN* 1.3 79.8 - - - +
158C LEU* 1.3 62.9 + - - +
159C TYR* 5.2 1.1 - - + -
174C LYS* 5.5 4.1 - - - +
176C TRP* 3.5 62.6 - - + -
177C TYR 3.4 5.2 - - - +
178C VAL* 4.2 4.9 - - - -
179C VAL* 4.5 2.2 - - - +
192C MET* 5.5 1.8 - - - +
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C GLY 3.4 12.1 - - - +
140C TYR* 4.2 24.0 - - + -
157C ARG* 1.3 73.7 - - - +
159C TYR* 1.3 60.0 + - - +
176C TRP* 3.2 2.1 - - - +
177C TYR* 2.8 48.4 + - + +
179C VAL* 3.8 27.8 - - + +
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Residues in contact with TYR 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLN* 3.3 29.6 + - - +
119C PHE* 3.4 17.2 - - - +
137C GLU* 2.7 34.3 + - + -
138C MET* 3.4 3.6 - - - +
139C GLY 3.0 58.3 + - - +
140C TYR 3.7 8.7 - - - -
141C ASN* 3.9 16.4 - - + -
157C ARG* 5.2 1.3 - - + -
158C LEU* 1.3 76.4 - - - +
160C THR* 1.3 72.7 + - - +
161C ARG* 3.8 7.9 - - + -
174C LYS* 3.5 29.6 - - + -
175C PRO 3.2 14.4 - - - +
176C TRP* 3.8 9.9 - - + -
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Residues in contact with THR 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C VAL* 5.0 2.0 - - + -
137C GLU 3.1 15.0 - - - +
138C MET* 3.7 24.3 - - + +
159C TYR* 1.3 80.2 + - - +
161C ARG* 1.3 69.4 + - - +
162C LEU* 4.1 23.6 - - + -
174C LYS* 3.2 7.4 - - - +
175C PRO* 3.0 39.8 + - - +
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Residues in contact with ARG 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY 5.5 1.2 + - - -
18A ILE* 3.8 25.2 - - - +
19A ILE* 3.9 5.1 - - - +
35C TYR* 3.7 16.1 + - - -
135C ASP* 2.8 35.2 + - - +
136C VAL* 3.6 2.8 - - - -
137C GLU* 2.7 75.1 + - + +
159C TYR* 3.8 12.2 - - + -
160C THR* 1.3 74.9 - - - +
162C LEU* 1.3 63.3 + - - +
163C MET* 3.7 20.8 - - - +
172C GLU* 3.0 46.6 + - + +
173C VAL 3.6 3.1 - - - +
174C LYS* 4.3 11.9 - - + +
198C LYS* 5.7 0.2 - - - +
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C LEU* 4.3 16.8 - - + -
135C ASP 3.4 2.0 - - - -
136C VAL* 3.9 27.6 - - + -
160C THR* 4.1 23.1 - - + -
161C ARG* 1.3 76.0 - - - +
163C MET* 1.3 61.1 + - - +
171C VAL 3.8 0.7 - - - +
172C GLU* 3.2 6.4 - - - +
173C VAL* 2.9 54.4 + - + +
175C PRO* 5.3 6.3 - - + -
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Residues in contact with MET 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.8 0.2 - - + -
15A ARG 4.5 4.3 - - - +
16A GLY* 3.6 8.7 - - - +
17A SER* 3.4 39.0 - - - +
133C LEU* 3.5 5.1 - - - +
134C ARG* 2.7 53.9 + - + -
135C ASP* 3.0 19.8 + - + +
161C ARG* 3.7 24.0 - - - +
162C LEU* 1.3 74.9 - - - +
164C ALA* 1.3 70.7 + - - +
165C GLU* 4.3 4.3 - - + -
170C LEU* 3.9 32.5 - - + -
171C VAL 3.5 3.4 - - - +
172C GLU* 4.6 4.5 - - + +
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Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C TRP* 3.8 20.5 - - + -
132C THR 3.0 17.9 - - - +
133C LEU* 4.0 11.9 - - + +
162C LEU 4.3 0.2 - - - -
163C MET* 1.3 78.7 - - - +
165C GLU* 1.3 61.1 + - - +
170C LEU* 3.5 2.4 - - - -
171C VAL* 2.8 36.4 + - + +
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Residues in contact with GLU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.6 5.3 - - + +
15A ARG 4.9 10.7 + - - +
130C GLY 4.1 0.7 - - - +
131C TRP* 3.4 4.2 - - - -
132C THR* 2.8 39.6 + - - -
134C ARG* 2.9 48.5 + - + +
163C MET* 4.4 9.9 - - + -
164C ALA* 1.3 75.6 - - - +
166C ASN* 1.3 67.5 + - - +
167C GLY 4.4 7.2 + - - +
169C TRP 3.3 14.1 - - - +
170C LEU* 4.5 5.4 - - + -
269C PHE* 5.8 2.0 - - + -
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Residues in contact with ASN 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ALA 4.4 1.4 + - - -
130C GLY* 3.4 25.0 + - - +
131C TRP* 3.4 45.9 - - + +
165C GLU* 1.3 79.3 - - - +
167C GLY* 1.3 68.0 + - - +
168C ASN 3.3 0.9 + - - -
169C TRP* 3.0 32.5 + - - +
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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