Contacts of the strand formed by residues 172 - 180 (chain A) in PDB entry 5H4Y
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 HIS 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A LEU 3.9 5.6 - - - +
131A GLN* 3.7 24.4 + - + -
165A HIS* 3.0 25.6 + - - -
170A ASN* 3.4 19.7 + - - +
171A PRO* 1.3 75.8 - - - +
173A PHE* 1.3 63.6 + - - +
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Residues in contact with PHE 173 (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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112A LEU* 4.2 1.8 - - + -
129A ILE* 3.3 31.6 - - + +
130A LEU 2.9 9.3 + - - +
131A GLN* 3.8 14.8 - - - -
132A ALA* 4.0 14.8 - - + -
146A PRO* 3.7 26.0 - - + -
147A TYR* 3.9 2.2 - - - -
148A VAL* 3.6 20.4 - - + -
162A THR* 3.6 28.7 - - + -
165A HIS* 3.7 23.6 + + - -
171A PRO* 3.4 32.3 - - + -
172A HIS* 1.3 75.5 - - - +
174A GLY* 1.3 63.8 + - - +
175A GLU* 3.3 15.8 + - + +
195A VAL* 5.2 1.3 - - + -
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Residues in contact with GLY 174 (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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129A ILE 3.1 10.1 + - - -
130A LEU* 3.2 10.1 + - - -
172A HIS 4.0 0.2 - - - -
173A PHE* 1.3 75.3 - - - +
175A GLU* 1.3 60.5 + - - +
176A THR* 5.1 0.6 + - - -
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Residues in contact with GLU 175 (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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127A VAL 4.6 0.2 - - - -
128A GLY* 3.3 1.0 - - - -
129A ILE* 2.8 32.2 + - + +
130A LEU* 5.2 0.7 - - - +
161A GLU 4.6 0.5 - - - +
162A THR* 3.4 35.0 - - + -
163A LYS* 2.8 40.6 + - - +
165A HIS* 5.1 1.4 - - - -
173A PHE* 3.6 18.5 - - + +
174A GLY* 1.3 78.2 - - - +
176A THR* 1.3 67.6 + - - +
177A PHE* 3.5 25.2 - - + -
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Residues in contact with THR 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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126A LEU* 4.3 20.0 - - + -
127A VAL 3.3 18.8 - - - +
128A GLY* 4.0 6.2 - - - +
174A GLY 4.4 1.8 + - - -
175A GLU* 1.3 78.2 + - - +
177A PHE* 1.3 80.7 + - - +
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Residues in contact with PHE 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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126A LEU* 3.5 1.9 - - - -
127A VAL* 2.8 33.7 + - + +
129A ILE* 4.4 6.5 - - + -
150A VAL* 3.9 31.4 - - + -
160A TYR* 3.6 43.7 - + + -
161A GLU 3.8 8.1 - - - -
162A THR* 3.8 31.2 - - + -
175A GLU* 3.5 30.5 - - + -
176A THR* 1.3 84.4 - - - +
178A ALA* 1.3 63.7 + - - +
179A PHE* 4.9 5.8 - - + -
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Residues in contact with ALA 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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124A GLN* 3.6 27.4 - - + +
125A LEU 3.1 12.3 - - - +
126A LEU* 3.9 14.1 - - + -
160A TYR* 3.7 20.5 + - - -
177A PHE* 1.3 79.5 - - - +
179A PHE* 1.3 70.5 + - - +
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Residues in contact with PHE 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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124A GLN* 3.2 4.6 - - - -
125A LEU* 2.8 45.1 + - + +
127A VAL* 3.9 24.0 - - + -
150A VAL* 3.8 21.5 - - + -
151A TYR* 3.7 16.6 - - - -
152A LEU* 3.8 41.5 - - + -
155A ASP* 6.0 1.1 - - + -
158A ARG* 3.5 29.6 - - + +
160A TYR* 3.5 29.4 - + - -
177A PHE* 4.9 0.7 - - + -
178A ALA* 1.3 82.9 - - - +
180A LYS* 1.3 64.0 + - - +
181A VAL* 3.4 2.9 + - - +
189A ARG* 5.4 2.9 - - - +
191A LEU* 4.2 5.4 - - + -
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Residues in contact with LYS 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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122A SER 3.8 19.5 + - - +
123A GLY* 3.6 11.7 - - - +
124A GLN* 4.3 14.6 + - + +
158A ARG* 4.2 27.0 + - - +
178A ALA 4.4 0.2 - - - -
179A PHE* 1.3 71.6 - - - +
181A VAL* 1.3 62.8 + - - +
182A PRO* 4.8 2.8 - - + +
189A ARG* 4.7 5.9 + - - -
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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