Contacts of the strand formed by residues 144 - 154 (chain H) in PDB entry 1DQD
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 MET 144 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141H THR 5.6 0.5 - - - +
142H ASN* 3.3 12.1 - - - +
143H SER* 1.3 98.1 + - - +
145H VAL* 1.3 64.3 + - - +
191H THR* 3.7 24.5 - - + +
192H VAL* 3.4 31.0 - - - +
193H PRO* 3.6 13.7 - - + -
194H SER* 4.3 2.1 + - - -
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Residues in contact with VAL 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H PRO* 4.4 13.7 - - + -
138H ALA* 6.2 4.0 - - + -
144H MET* 1.3 75.8 - - - +
146H THR* 1.3 65.1 + - - +
147H LEU* 3.9 23.7 + - + -
190H VAL 3.8 1.0 - - - +
191H THR* 3.2 2.1 - - - -
192H VAL* 2.7 57.1 + - + +
193H PRO 4.3 0.2 - - - +
194H SER* 4.1 20.4 - - - -
197H TRP* 4.3 17.7 - - + +
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Residues in contact with THR 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H PRO* 4.5 3.6 - - - +
145H VAL* 1.3 73.3 - - - +
147H LEU* 1.3 76.4 + - - +
189H SER* 4.2 16.6 - - - -
190H VAL 3.4 7.0 - - - +
191H THR* 3.3 24.2 + - - +
113L THR* 4.9 9.5 - - - +
115L SER* 3.4 26.6 + - - +
117L PHE* 2.9 28.0 - - + -
134L PHE* 4.3 7.0 - - + -
136L ASN* 4.5 7.7 + - - +
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Residues in contact with LEU 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H LEU 3.7 11.2 - - - +
134H ALA* 4.9 0.2 - - - -
135H PRO* 3.5 24.5 - - + -
145H VAL* 3.9 14.6 - - + +
146H THR* 1.3 87.6 - - - +
148H GLY* 1.3 57.6 + - - +
189H SER* 3.4 6.5 - - - -
190H VAL* 2.8 39.1 + - + +
192H VAL* 5.1 3.8 - - + -
197H TRP* 3.4 44.4 - - + -
202H VAL* 3.4 33.0 - - + -
219H ILE* 4.5 9.4 - - + -
117L PHE* 3.9 5.6 - - - -
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Residues in contact with GLY 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H LEU* 3.0 41.5 + - - +
147H LEU* 1.3 75.6 - - - +
149H CYS* 1.3 67.8 + - - -
163H TRP* 3.5 12.9 - - - -
188H SER 3.1 13.5 - - - -
189H SER* 4.1 0.7 - - - -
219H ILE* 3.5 5.7 - - - +
134L PHE* 4.4 2.0 - - - -
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Residues in contact with CYS 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H VAL* 4.7 5.2 - - + -
131H TYR 3.2 13.0 - - - +
132H PRO* 4.5 0.4 - - - -
133H LEU* 3.5 5.5 - - - +
148H GLY* 1.3 80.8 - - - -
150H LEU* 1.3 60.6 + - - +
151H VAL* 4.1 4.4 - - + +
161H VAL* 5.6 0.9 - - + -
163H TRP* 3.8 3.7 - - + -
187H SER* 3.2 8.0 - - - -
188H SER* 3.0 33.6 + - - +
204H CYS* 2.0 53.2 - - + -
206H VAL* 4.9 3.8 - - + -
217H LYS* 4.6 0.9 - - - -
219H ILE* 3.4 18.2 - - - -
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Residues in contact with LEU 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H SER 3.1 6.1 - - - +
130H VAL* 3.3 1.6 - - - -
131H TYR* 2.8 61.7 + - + +
133H LEU* 4.1 18.4 - - + +
149H CYS* 1.3 71.9 - - - +
151H VAL* 1.3 59.8 + - - +
152H LYS* 4.3 11.0 - - + -
185H THR* 3.8 19.1 - - + -
186H LEU 3.7 13.7 - - - +
187H SER* 4.6 4.5 - - - -
123L GLN* 4.0 15.0 - - - +
130L SER* 4.3 15.7 - - - +
132L VAL* 4.4 9.2 - - + -
177L THR* 4.2 21.8 - - + -
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Residues in contact with VAL 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H PRO* 3.4 29.8 - - + -
129H SER 3.5 3.6 - - - -
130H VAL* 4.3 3.6 - - + -
149H CYS* 4.8 3.8 - - + -
150H LEU* 1.3 78.2 - - - +
152H LYS* 1.3 59.0 + - - +
154H TYR* 3.6 12.5 - - + -
159H VAL* 4.1 11.2 - - + -
161H VAL* 4.4 4.5 - - + -
185H THR* 3.3 3.8 - - - -
186H LEU* 2.8 58.4 + - + +
188H SER 5.8 0.2 - - - +
206H VAL* 4.0 34.8 - - + -
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Residues in contact with LYS 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H PRO* 3.6 0.6 - - - +
129H SER* 2.9 44.8 + - - +
131H TYR* 5.1 6.7 - - + -
150H LEU* 3.7 15.0 + - + -
151H VAL* 1.3 75.6 - - - +
153H GLY* 1.3 69.8 + - - +
154H TYR 3.5 1.8 - - - -
180H GLN* 3.5 32.6 + - - +
185H THR* 3.4 24.2 + - + +
123L GLN* 4.8 9.0 - - - +
130L SER* 4.6 10.1 - - - +
179L THR* 3.9 30.1 + - - +
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Residues in contact with GLY 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H THR* 3.4 23.9 - - - +
127H PRO 3.5 4.1 - - - +
152H LYS* 1.3 84.6 - - - +
154H TYR* 1.3 59.8 + - - +
183H LEU* 3.7 31.3 - - - +
184H TYR 2.9 9.4 + - - -
185H THR* 3.4 2.2 + - - -
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Residues in contact with TYR 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H THR 3.1 11.7 - - - +
128H PRO* 3.4 21.5 - - + -
151H VAL* 3.6 33.4 - - + -
153H GLY* 1.3 74.5 - - - +
155H PHE* 1.3 64.2 + - - +
156H PRO 3.6 20.2 - - - -
157H GLU* 2.9 28.2 + - - -
159H VAL* 3.3 30.9 - - + +
177H ALA* 3.2 16.8 - - - +
183H LEU* 3.8 1.8 - - - -
184H TYR* 2.8 75.7 + - + +
185H THR 4.0 1.1 - - - -
186H LEU* 3.6 17.8 - - + +
208H HIS* 4.0 4.0 - + - +
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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