Contacts of the strand formed by residues 173 - 182 (chain L) in PDB entry 4G5Z
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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H HIS* 5.8 0.9 - - - -
105L ASP* 2.5 43.6 + - - +
138L ASN* 3.3 4.4 + - - -
139L PHE* 2.8 58.7 + - + +
140L TYR* 4.0 13.9 - + - -
142L ARG* 3.3 56.7 + - + -
163L VAL* 4.4 8.5 - - + -
164L THR* 3.4 23.1 - - - +
165L GLU 4.0 0.4 - - - -
166L GLN* 3.5 36.5 - - + +
172L THR* 1.3 76.1 - - - +
174L SER* 1.3 62.2 + - - +
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Residues in contact with SER 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H HIS* 3.3 21.3 + - - -
171H PHE* 3.5 17.6 - - - -
136L LEU 3.3 9.6 - - - -
137L ASN* 3.0 24.3 + - - -
138L ASN* 3.1 13.7 + - - -
139L PHE* 3.8 2.5 - - - -
163L VAL* 3.4 4.4 - - - +
164L THR* 2.9 38.6 + - - -
173L TYR* 1.3 72.0 + - - +
175L LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H PHE* 3.6 4.3 - - - -
134L CYS 3.9 0.2 - - - +
135L LEU* 3.7 2.6 - - - +
136L LEU* 2.8 49.1 + - + +
139L PHE* 3.6 21.0 - - + -
142L ARG 5.6 1.8 - - - +
144L ALA* 4.5 13.9 - - + +
146L VAL* 3.8 27.6 - - + -
161L GLU* 3.6 28.9 - - + +
162L SER 3.4 13.2 - - - +
163L VAL* 4.2 17.3 - - + -
174L SER* 1.3 74.1 - - - +
176L SER* 1.3 77.6 + - - +
177L SER 4.1 0.9 - - - +
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Residues in contact with SER 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H PHE* 3.6 33.8 - - - -
184H SER* 4.2 12.9 + - - -
186H VAL* 5.6 1.0 - - - +
133L VAL* 3.5 23.2 - - - +
134L CYS 3.5 3.1 + - - -
135L LEU* 4.7 3.0 - - - +
160L GLN 4.1 0.5 - - - +
161L GLU* 3.2 3.1 - - - +
162L SER* 2.9 34.9 + - - -
175L LEU* 1.3 76.5 - - - +
177L SER* 1.3 60.0 + - - +
178L THR* 4.7 5.0 + - - -
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Residues in contact with SER 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133L VAL* 3.4 2.9 - - - +
134L CYS* 2.8 41.2 + - - -
146L VAL* 3.8 30.7 - - - +
148L TRP* 2.9 29.4 + - - -
159L SER* 4.3 4.9 + - - -
160L GLN 3.5 8.0 + - - -
161L GLU* 4.1 13.1 + - - +
176L SER* 1.3 73.8 - - - +
178L THR* 1.3 62.1 + - - +
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Residues in contact with THR 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H LEU* 4.9 8.9 - - + +
174H VAL* 6.4 2.5 - - - -
182H SER* 5.7 2.1 + - - +
184H SER* 4.6 7.8 + - - -
131L SER* 3.8 26.0 - - - -
132L VAL 3.3 8.5 - - - +
133L VAL* 3.9 17.3 - - + +
148L TRP* 4.4 0.2 - - - -
159L SER* 3.2 6.3 - - - -
160L GLN* 2.8 39.7 + - - +
176L SER* 4.7 3.8 + - - -
177L SER* 1.3 73.8 + - - +
179L LEU* 1.3 62.2 + - - +
180L THR* 3.9 14.3 + - - +
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Residues in contact with LEU 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L ALA 3.5 1.9 - - - +
131L SER* 3.4 3.3 - - - -
132L VAL* 2.8 43.7 + - + +
148L TRP* 3.7 54.9 - - + -
150L VAL* 4.1 10.3 - - + -
155L GLN* 4.3 2.7 - - + -
158L ASN* 3.3 41.1 - - - +
159L SER* 4.3 1.3 - - - -
178L THR* 1.3 70.8 - - - +
180L THR* 1.3 59.9 + - - +
181L LEU* 4.0 24.9 - - + -
192L TYR* 4.0 18.6 - - + -
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Residues in contact with THR 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H LYS* 4.6 9.6 - - - +
176H GLN* 5.3 5.9 + - - +
129L THR* 3.9 24.9 - - + -
130L ALA 3.6 4.3 - - - +
131L SER* 4.2 7.7 + - - +
158L ASN* 3.0 27.4 + - - +
178L THR* 3.9 18.4 + - - +
179L LEU* 1.3 73.5 - - - +
181L LEU* 1.3 68.0 + - - +
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Residues in contact with LEU 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L THR* 3.7 7.2 - - - +
130L ALA* 2.9 33.9 + - + +
132L VAL* 5.4 2.5 - - + -
150L VAL* 5.1 3.6 - - + -
155L GLN* 5.1 3.4 - - - +
158L ASN* 4.0 21.8 - - + +
179L LEU* 4.0 16.6 - - + -
180L THR* 1.3 78.3 - - - +
182L SER* 1.3 68.5 + - - +
185L ASP* 4.0 24.7 - - + +
186L TYR* 4.3 10.8 - - + +
189L HIS* 5.3 6.7 - - + +
192L TYR* 3.7 36.3 - - + +
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Residues in contact with SER 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L GLY 3.7 9.9 - - - -
129L THR* 4.6 2.5 - - - +
130L ALA 4.5 0.7 - - - -
181L LEU* 1.3 76.8 - - - +
183L LYS* 1.3 63.3 + - - +
184L ALA* 3.8 7.0 + - - +
185L ASP* 3.2 33.5 + - - +
186L TYR* 2.9 21.9 + - - +
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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