Contacts of the strand formed by residues 174 - 180 (chain A) in PDB entry 5HH0
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 GLY 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A HIS* 6.3 0.9 - - - -
139A VAL 3.2 13.2 - - - -
140A LEU* 5.4 0.2 - - - -
141A THR* 3.9 7.4 - - - -
160A TYR* 3.5 9.9 - - - -
161A LEU* 2.8 38.7 + - - +
173A ASP* 1.3 77.5 - - - +
175A PHE* 1.3 64.4 + - - -
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Residues in contact with PHE 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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138A HIS* 3.4 8.6 - - - +
139A VAL* 2.9 40.1 + - + +
141A THR* 3.8 34.1 - - + -
147A ILE* 4.3 10.8 - - + -
157A GLN* 3.5 43.3 - - + -
159A HIS 3.5 3.8 - - - +
160A TYR* 3.8 32.1 - + + -
161A LEU* 4.4 1.3 - - - +
174A GLY* 1.3 78.3 - - - -
176A THR* 1.3 61.4 + - - +
177A TYR* 3.6 21.0 + + + -
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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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81A ASP* 2.7 37.4 + - - +
84A ILE* 4.3 4.7 - - + -
136A TYR* 4.3 6.7 - - + -
137A LEU 3.4 9.6 - - - +
138A HIS* 3.2 14.5 - - + -
157A GLN* 3.7 4.2 - - - -
158A HIS* 2.8 29.7 + - + -
159A HIS* 3.0 21.3 + - - +
161A LEU* 3.4 7.8 - - - +
175A PHE* 1.3 73.4 - - - +
177A TYR* 1.3 64.9 + - - +
178A VAL* 4.0 19.5 - - + -
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Residues in contact with TYR 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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136A TYR* 3.2 4.0 - - - +
137A LEU* 2.9 49.2 + - + +
139A VAL* 3.8 28.0 - - + -
147A ILE* 3.4 20.9 - - + +
150A TYR* 4.7 7.2 - - + -
151A GLU* 2.7 40.2 + - + -
155A PHE* 4.1 21.9 - - + -
156A LYS 3.2 19.1 - - - -
157A GLN* 3.0 37.3 + - + -
175A PHE* 3.6 21.1 - - + -
176A THR* 1.3 75.5 - - - +
178A VAL* 1.3 65.5 - - - +
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Residues in contact with VAL 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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84A ILE* 3.8 29.4 - - + -
134A ALA* 3.8 15.5 - - + -
135A ILE 3.4 10.3 - - - +
136A TYR* 3.9 8.1 - - + -
154A ASP 4.2 0.7 - - - +
155A PHE* 3.3 3.9 - - - -
156A LYS* 2.8 40.8 + - + +
158A HIS* 3.9 17.3 - - + -
176A THR* 4.0 2.2 - - + -
177A TYR* 1.3 81.2 - - - +
179A LEU* 1.3 62.3 + - - +
180A TYR* 3.7 39.3 + - + +
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Residues in contact with LEU 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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121A LYS* 4.0 29.4 - - - +
134A ALA* 3.4 1.2 - - - -
135A ILE* 2.9 53.6 + - + +
153A ARG 3.9 3.6 - - - +
154A ASP* 3.5 39.7 - - + +
155A PHE* 3.4 34.0 - - + -
178A VAL* 1.3 75.6 - - - +
180A TYR* 1.3 71.7 - - - +
181A ILE* 3.8 9.5 + - + +
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Residues in contact with TYR 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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84A ILE* 2.6 34.4 + - - -
85A LEU* 4.2 6.5 - - + -
133A LYS 3.7 9.2 - - - -
134A ALA* 4.1 4.5 - - + -
156A LYS* 5.4 12.6 - - + -
158A HIS* 4.2 7.8 + - - -
178A VAL* 3.7 30.8 - - + +
179A LEU* 1.3 82.4 - - - +
181A ILE* 1.3 66.0 + - - +
184A GLY 3.2 34.1 - - - +
185A HIS* 3.7 9.6 - - - -
186A PRO* 3.5 27.6 - - + +
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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