Contacts of the strand formed by residues 146 - 156 (chain H) in PDB entry 6AL5
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 THR 146 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H GLY* 1.3 87.0 + - - +
147H ALA* 1.3 61.5 + - - +
194H THR* 5.0 8.6 - - - +
195H VAL 3.5 13.9 - - - +
196H PRO* 4.4 8.3 - - + -
197H SER* 4.0 1.7 + - - -
120L PHE* 4.4 15.5 - - - -
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Residues in contact with ALA 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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137H PRO* 4.5 10.5 - - + -
138H SER 5.4 6.5 - - - +
146H THR* 1.3 75.0 - - - +
148H ALA* 1.3 60.5 + - - +
193H VAL 3.8 0.2 - - - +
194H THR* 3.0 4.7 - - - -
195H VAL* 2.6 51.9 + - + +
197H SER* 4.1 9.8 + - - +
200H LEU* 4.0 26.9 - - + -
120L PHE* 4.5 4.0 - - - -
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Residues in contact with ALA 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H PRO* 3.2 18.6 - - - +
147H ALA* 1.3 76.6 - - - +
149H LEU* 1.3 60.8 + - - +
193H VAL 3.2 8.1 - - - +
194H THR* 3.8 10.1 - - + -
120L PHE* 3.7 43.5 - - + -
122L PHE* 3.5 15.3 - - + -
139L LEU* 4.3 12.6 - - + -
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Residues in contact with LEU 149 (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 LEU 3.4 7.4 - - - +
137H PRO* 3.5 34.1 - - + -
148H ALA* 1.3 74.6 - - - +
150H GLY* 1.3 57.1 + - - +
165H TRP* 3.8 22.2 - - + -
192H VAL* 3.2 7.0 - - - +
193H VAL* 2.7 57.6 + - + +
195H VAL* 4.0 26.0 - - + -
200H LEU* 4.4 5.2 - - + -
205H TYR* 3.9 27.1 - - + -
222H VAL* 4.1 12.3 - - + +
122L PHE* 4.3 4.0 - - - -
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Residues in contact with GLY 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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134H PRO 3.6 0.2 - - - -
135H LEU* 2.7 43.5 + - - +
149H LEU* 1.3 79.0 - - - +
151H CYS* 1.3 62.3 - - - -
165H TRP* 3.6 11.0 - - - -
191H SER 3.1 12.8 - - - -
192H VAL* 3.8 3.4 - - - -
222H VAL* 3.6 11.1 - - - +
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Residues in contact with CYS 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H VAL* 4.4 6.5 - - + -
133H PHE 3.5 4.9 - - - +
135H LEU* 4.0 6.2 - - - +
150H GLY* 1.3 76.5 - - - -
152H LEU* 1.3 61.0 + - - +
153H VAL* 4.0 9.0 + - + +
163H VAL* 5.3 0.7 - - + -
165H TRP* 3.6 10.8 - - + -
190H SER* 3.4 4.5 - - - -
191H SER* 2.7 38.2 + - - +
207H CYS* 2.0 52.3 - - + -
209H VAL* 5.1 0.2 - - + -
220H LYS* 4.3 9.2 - - - -
222H VAL* 3.9 11.2 - - - -
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Residues in contact with LEU 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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131H SER 3.5 2.4 - - - +
132H VAL* 3.4 4.9 - - - +
133H PHE* 2.7 57.6 + - + +
135H LEU* 4.0 20.8 - - + +
151H CYS* 1.3 71.6 - - - +
153H VAL* 1.3 60.8 + - - +
154H LYS* 3.7 16.5 + - + -
188H SER* 4.2 12.6 - - - +
189H LEU 3.5 18.4 - - - +
190H SER* 4.4 9.4 - - - +
128L GLN* 4.7 2.0 - - - +
135L SER* 3.7 32.8 - - - +
137L VAL* 4.5 14.1 - - + -
182L THR* 4.9 7.6 - - + +
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Residues in contact with VAL 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H PRO* 3.5 29.6 - - + -
131H SER 3.7 2.5 - - - -
132H VAL* 4.4 5.6 - - + -
151H CYS* 4.6 8.3 - - + +
152H LEU* 1.3 74.9 - - - +
154H LYS* 1.3 58.6 + - - +
156H TYR* 3.6 15.1 - - + -
161H VAL* 4.3 8.1 - - + -
163H VAL* 4.3 6.7 - - + -
188H SER* 3.4 4.4 - - - -
189H LEU* 2.8 55.1 + - + +
191H SER 5.7 0.2 - - - +
209H VAL* 4.0 35.2 - - + -
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Residues in contact with LYS 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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130H PRO* 3.4 2.1 - - - +
131H SER* 2.9 38.5 + - - +
133H PHE* 4.5 13.7 - - + -
152H LEU* 4.3 14.1 - - + -
153H VAL* 1.3 73.3 - - - +
155H ASP* 1.3 94.5 + - - +
156H TYR 3.7 1.1 - - - -
182H GLN* 3.2 24.8 + - - +
188H SER* 3.5 14.6 - - - +
128L GLN* 4.0 9.4 - - - +
133L THR* 4.4 17.0 - - - +
135L SER* 3.3 27.8 - - - +
182L THR* 5.5 4.0 - - + -
184L THR* 4.6 12.5 - - - +
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Residues in contact with ASP 155 (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 LYS* 3.3 21.5 + - - +
129H GLY 3.1 18.5 - - - +
131H SER* 5.1 5.6 + - - +
133H PHE* 5.6 1.9 - - - -
154H LYS* 1.3 101.0 + - - +
156H TYR* 1.3 57.8 + - - +
182H GLN* 3.0 20.8 + - - +
184H SER* 4.7 2.3 + - - -
186H LEU* 3.7 28.0 - - + +
187H TYR 3.1 10.9 + - - -
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Residues in contact with TYR 156 (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 LYS 3.4 11.4 - - - +
130H PRO* 3.6 20.9 - - + -
153H VAL* 3.6 31.0 - - + -
155H ASP* 1.3 74.3 - - - +
157H PHE* 1.3 61.8 + - - +
158H PRO 3.6 21.8 - - - -
159H GLU* 3.2 14.1 + - - -
161H VAL* 3.5 35.2 - - + +
179H ALA* 3.2 24.6 - - - +
186H LEU* 3.7 2.6 - - - -
187H TYR* 2.7 80.2 + - + +
188H SER* 3.9 3.6 - - - -
189H LEU* 3.4 14.5 - - + +
211H HIS* 4.0 3.4 - - - +
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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