Contacts of the strand formed by residues 173 - 182 (chain A) in PDB entry 5I7L
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 ILE 173 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ALA* 4.4 0.4 - - + -
166A VAL 3.5 14.1 - - - +
167A ARG* 4.2 15.7 - - - +
171A GLU* 5.1 3.8 - - - +
172A ARG* 1.3 79.1 - - - +
174A HIS* 1.3 66.8 + - - +
175A LEU 4.3 0.3 + - - -
240A HIS* 5.9 3.4 - - + -
243A VAL* 3.4 39.6 - - + +
244A ASN* 4.6 9.2 - - - +
247A ILE* 3.3 48.7 - - + -
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Residues in contact with HIS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ALA* 3.2 6.1 - - - -
166A VAL* 2.9 40.2 + - + +
168A ASP* 3.2 40.9 + - + +
172A ARG* 4.0 27.4 + - + +
173A ILE* 1.3 77.6 + - - +
175A LEU* 1.3 63.0 + - - +
176A VAL* 3.6 15.7 + - + +
243A VAL* 3.8 4.0 - - - -
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 5.9 0.7 - - + -
163A ILE* 3.5 20.4 - - + -
164A LEU 3.5 13.2 - - - +
173A ILE 4.3 0.6 + - - -
174A HIS* 1.3 71.7 - - - +
176A VAL* 1.3 61.7 + - - +
177A LEU 4.3 0.7 + - - -
231A LEU* 3.8 33.5 - - + +
234A LEU* 4.4 13.0 - - + -
239A VAL* 4.4 25.1 - - + +
242A ILE* 4.0 24.2 - - + -
243A VAL* 3.5 23.5 - - + +
246A LEU* 4.4 4.5 - - + -
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE* 3.5 5.5 - - - +
164A LEU* 2.9 44.1 + - + +
166A VAL* 3.5 33.2 - - + -
174A HIS* 3.9 10.3 - - + +
175A LEU* 1.3 77.7 - - - +
177A LEU* 1.3 78.0 + - - +
178A GLY* 3.3 4.5 + - - +
231A LEU* 4.3 3.1 - - - -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA* 3.8 29.2 - - + -
162A GLU 3.7 10.3 - - - +
163A ILE* 5.0 1.3 - - + -
175A LEU 4.3 0.4 + - - -
176A VAL* 1.3 81.2 - - - +
178A GLY* 1.3 66.9 + - - +
179A ASP 3.9 6.7 - - - +
180A CYS* 4.2 13.2 - - + -
224A CYS* 3.8 14.4 - - + +
227A VAL* 4.1 4.5 - - + -
228A ASN* 3.8 41.7 + - + +
231A LEU* 3.5 26.0 - - + +
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Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLU* 2.7 22.8 + - - -
164A LEU* 4.2 15.9 - - - +
176A VAL* 3.3 5.3 + - - -
177A LEU* 1.3 81.7 - - - +
179A ASP* 1.3 66.3 + - - -
180A CYS* 3.7 1.6 + - - +
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Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A THR* 4.3 4.0 - - + +
162A GLU* 2.9 52.5 + - + +
177A LEU* 3.9 1.9 - - - +
178A GLY* 1.3 75.6 - - - +
180A CYS* 1.3 62.3 + - - +
181A THR* 4.8 14.1 - - + +
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Residues in contact with CYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.7 15.3 - - - -
160A THR 3.3 4.5 - - - -
161A ALA* 4.1 15.3 - - - -
177A LEU* 4.2 17.7 - - + -
178A GLY 3.7 1.7 + - - +
179A ASP* 1.3 76.8 - - - +
181A THR* 1.3 61.4 + - - +
220A GLN* 3.5 13.9 + - - -
224A CYS* 2.1 60.0 - - + +
227A VAL* 4.6 2.9 - - - -
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.4 8.3 - - - +
160A THR* 2.8 41.6 + - - +
179A ASP* 4.2 14.7 - - + +
180A CYS* 1.3 85.1 - - - +
182A HIS* 1.3 70.8 + - - +
183A SER* 5.2 0.2 - - - -
184A PRO* 5.2 1.7 - - - +
220A GLN* 3.3 17.5 - - - +
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Residues in contact with HIS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 4.5 6.1 - - + -
158A ASP 3.5 8.1 - - - +
159A ILE* 3.8 9.1 - - + +
181A THR* 1.3 87.8 + - - +
183A SER* 1.3 62.0 + - - +
184A PRO* 3.2 27.1 - - + +
216A PRO* 3.3 49.1 - - + +
217A GLU* 4.0 20.6 + - + -
220A GLN* 3.2 22.5 + - - -
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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