Contacts of the strand formed by residues 173 - 182 (chain H) in PDB entry 3SKJ
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 TYR 173 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H THR* 5.2 7.6 - - - +
141H ASP 2.8 30.8 + - - -
142H TYR* 2.7 47.9 + - + +
143H PHE* 3.7 32.1 - + - -
144H PRO* 5.3 0.2 - - + -
145H GLU* 3.5 50.1 + - + -
165H ALA* 3.6 21.3 - - + -
166H VAL 3.4 10.3 - - - -
167H LEU* 3.9 33.6 - - + +
168H GLN* 3.2 2.4 + - - -
172H LEU* 1.3 75.4 - - - +
174H SER* 1.3 55.8 - - - +
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Residues in contact with SER 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H LEU* 3.8 12.0 - - - +
139H VAL 3.4 10.9 + - - -
140H LYS* 3.7 18.1 + - - +
142H TYR* 4.1 1.3 - - - -
164H PRO 4.4 0.9 - - - +
165H ALA* 3.5 1.0 - - - -
166H VAL* 2.9 42.3 + - - +
168H GLN* 3.2 27.8 - - - -
173H TYR* 1.3 71.5 - - - +
175H LEU* 1.3 64.7 + - - +
160L GLN* 5.8 0.7 - - - -
178L THR* 6.0 1.2 - - - +
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Residues in contact with LEU 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H LEU* 3.6 6.3 - - - +
139H VAL* 2.7 61.0 + - + +
142H TYR* 3.6 22.2 - - + +
147H VAL* 4.0 21.3 - - + +
149H VAL* 4.3 4.3 - - + -
162H THR* 4.1 17.3 - - + -
163H PHE* 3.3 25.8 - - - +
164H PRO 4.9 2.0 - - - -
165H ALA* 4.3 9.9 - - + +
174H SER* 1.3 76.8 + - - +
176H SER* 1.3 70.7 + - - +
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Residues in contact with SER 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 3.6 21.9 - - - +
137H CYS 3.2 5.3 + - - -
138H LEU* 3.6 19.9 - - - +
162H THR* 3.8 0.9 - - - -
163H PHE* 3.0 45.9 + - - +
175H LEU* 1.3 79.2 - - - +
177H SER* 1.3 60.2 + - - +
178H VAL* 4.9 3.1 - - - -
133L VAL* 4.7 8.1 - - - +
176L SER* 4.6 11.0 - - - -
178L THR* 5.0 1.9 + - - -
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Residues in contact with SER 177 (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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136H GLY* 3.2 3.5 - - - -
137H CYS* 2.9 36.5 + - - +
139H VAL* 6.0 0.4 - - - -
149H VAL* 3.8 25.1 - - - +
151H TRP* 3.1 25.4 + - - -
160H VAL* 4.0 1.6 - - - +
161H HIS 3.4 4.8 + - - -
162H THR* 3.1 27.4 + - - +
175H LEU* 4.4 0.8 - - - +
176H SER* 1.3 73.4 - - - +
178H VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 4.2 18.2 - - + -
135H LEU 3.3 13.2 - - - +
136H GLY* 4.2 0.4 - - - -
151H TRP* 4.6 0.9 - - - -
159H GLY 3.8 0.2 - - - +
160H VAL* 3.3 3.8 - - - +
161H HIS* 2.7 66.4 + - + +
163H PHE* 3.9 15.7 - - + -
176H SER* 4.9 2.9 - - - -
177H SER* 1.3 81.5 + - - +
179H VAL* 1.3 63.0 + - - +
180H THR* 6.2 1.6 - - + -
118L PHE* 5.2 3.1 - - + -
133L VAL* 6.1 2.2 - - + -
135L LEU* 3.9 37.0 - - + -
137L ASN* 4.8 1.3 - - - +
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Residues in contact with VAL 179 (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 ALA* 3.5 1.8 - - - -
135H LEU* 3.1 54.3 + - + +
151H TRP* 3.9 25.6 - - + -
156H LEU* 4.2 19.7 - - + -
158H SER 4.4 3.8 - - - +
159H GLY 3.2 7.0 - - - +
160H VAL* 3.0 42.2 - - + -
178H VAL* 1.3 73.2 - - - +
180H THR* 1.3 67.8 + - - +
181H VAL* 4.3 5.1 - - + +
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Residues in contact with THR 180 (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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132H THR* 5.1 9.5 - - - +
133H ALA 3.2 9.4 - - - -
134H ALA* 4.2 13.0 - - + +
156H LEU* 6.0 0.9 - - - +
158H SER 4.8 5.4 - - - +
159H GLY* 3.4 17.1 + - - +
161H HIS* 5.7 1.3 - - + +
178H VAL* 6.2 1.8 - - + -
179H VAL* 1.3 75.2 - - - +
181H VAL* 1.3 72.6 + - - +
116L PHE* 5.0 5.2 - - + -
135L LEU* 5.7 0.4 - - + -
137L ASN* 3.2 33.9 - - - +
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Residues in contact with VAL 181 (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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132H THR* 3.6 5.8 - - - -
133H ALA* 2.6 49.9 + - + +
135H LEU* 4.3 22.2 - - + -
156H LEU* 5.1 6.5 - - + -
179H VAL* 4.3 15.7 - - + +
180H THR* 1.3 88.8 + - - +
182H PRO* 1.3 75.5 - - + +
186H LEU* 4.3 11.4 - - + -
191H TYR* 3.7 34.8 - - + +
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Residues in contact with PRO 182 (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 GLY 4.2 4.9 - - - +
132H THR* 4.3 6.7 - - + -
181H VAL* 1.3 88.4 - - + +
183H SER* 1.3 66.1 + - - +
184H SER* 3.8 16.2 - - - +
185H SER* 3.0 39.0 + - - +
186H LEU* 4.2 0.3 + - - +
191H TYR* 4.8 0.9 - - - +
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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