Contacts of the strand formed by residues 154 - 159 (chain A) in PDB entry 2HDH
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 PHE 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.7 31.4 - + + -
132A PHE* 3.3 37.0 - + + -
134A SER* 4.5 7.4 - - - -
141A ILE* 3.9 17.7 - - + -
144A ILE* 3.6 26.7 - - + -
145A ALA* 3.6 39.0 - - + -
148A THR* 4.4 8.3 - - + -
150A ARG 3.8 6.7 - - - +
151A GLN* 3.2 15.5 + - - +
152A ASP 3.3 0.8 + - - -
153A ARG* 1.3 79.9 - - - +
155A ALA* 1.3 83.9 + - - +
174A THR* 4.4 2.4 + - - +
177A THR* 2.8 29.0 + - - +
181A THR* 4.8 0.2 - - - -
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Residues in contact with ALA 155 (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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132A PHE 3.1 7.2 + - - +
133A ALA* 3.3 6.2 - - - -
134A SER 3.2 19.8 + - - -
141A ILE* 3.7 12.0 - - - +
154A PHE* 1.3 86.0 - - - +
156A GLY* 1.3 61.1 + - - +
171A VAL* 5.5 0.7 - - + -
172A ILE 3.3 13.7 - - - +
177A THR* 3.9 17.0 - - + -
181A THR* 4.4 1.1 - - + -
182A PHE* 6.2 0.2 - - - -
185A LEU* 3.6 29.2 - - + -
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Residues in contact with GLY 156 (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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133A ALA* 4.9 0.2 - - - -
134A SER 3.5 9.9 - - - -
141A ILE* 3.6 18.6 - - - +
155A ALA* 1.3 76.8 - - - +
157A LEU* 1.3 60.7 + - - +
158A HIS* 3.9 1.6 - - - -
171A VAL* 3.4 8.3 - - - +
172A ILE* 2.7 46.5 + - - +
185A LEU* 4.6 0.7 - - - +
205A PHE* 6.3 0.2 - - - -
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Residues in contact with LEU 157 (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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103A LEU* 4.4 0.4 - - + -
105A VAL* 4.2 16.5 - - + +
133A ALA* 4.0 14.1 - - + -
134A SER 3.0 8.9 + - - +
135A ASN* 3.4 21.0 + - - +
155A ALA 4.2 0.8 + - - -
156A GLY* 1.3 74.1 - - - +
158A HIS* 1.3 58.2 + - - +
159A PHE* 3.4 34.0 - - + -
169A VAL* 3.5 20.9 - - + -
170A GLU 3.4 0.9 - - - -
171A VAL* 4.1 14.1 - - + -
185A LEU* 4.3 23.1 - - + +
188A PHE* 4.1 24.7 - - + -
189A SER* 3.8 15.5 - - - +
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Residues in contact with HIS 158 (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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134A SER 5.5 0.4 - - - +
135A ASN* 3.2 31.0 - - - +
136A THR 3.6 7.0 - - - +
137A SER* 2.9 22.3 + - - -
157A LEU* 1.3 71.2 - - - +
159A PHE* 1.3 66.4 + - - +
160A PHE* 3.6 16.1 - + - -
169A VAL* 3.4 5.1 - - - -
170A GLU* 2.8 67.4 + - + +
172A ILE* 4.9 1.6 - - + -
205A PHE* 3.5 23.7 - + + -
208A ASN* 3.5 27.6 - - - -
350A NAD 3.4 10.8 - + - -
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Residues in contact with PHE 159 (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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26A MSE 3.6 16.4 - - + -
30A ILE* 3.7 33.0 - - + -
105A VAL* 4.4 5.8 - - + -
135A ASN* 2.8 14.1 + - - -
157A LEU* 3.4 48.0 - - + -
158A HIS* 1.3 77.8 + - - +
160A PHE* 1.3 72.6 + - - +
163A VAL* 4.0 24.2 - - + -
166A MSE 6.1 0.2 - - - -
168A LEU 4.5 4.3 - - - -
169A VAL* 3.9 18.6 - - + -
188A PHE* 4.9 1.1 - + - -
192A LEU* 3.9 28.9 - - + -
194A LYS* 4.9 9.9 - - + -
350A NAD 3.4 21.7 - - - -
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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