Contacts of the strand formed by residues 156 - 163 (chain A) in PDB entry 1H1B
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 GLN 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.7 25.8 + - + +
19A GLY* 3.8 7.9 + - - +
20A ARG* 3.1 34.5 - - - +
21A ARG* 3.4 34.6 + - - +
22A ALA 4.6 0.9 - - - -
139A MET* 3.1 7.6 - - - +
140A GLY 3.1 32.3 + - - +
144A LEU* 4.1 18.4 - - + +
152A ALA* 3.9 15.7 - - + +
154A VAL 3.3 18.0 - - - +
155A LEU* 1.3 75.9 - - - +
157A GLU* 1.3 62.4 + - - +
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Residues in contact with GLU 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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16A ILE* 4.5 1.3 - - - -
19A GLY* 3.2 4.0 - - - -
20A ARG* 2.7 80.8 + - + +
21A ARG 4.6 0.7 - - - -
22A ALA* 3.5 19.6 - - + +
23A ARG 4.5 1.7 + - - -
27A TRP* 3.2 28.0 + - - +
137A LEU* 4.0 21.4 - - + +
138A ALA 3.4 9.9 - - - +
139A MET* 4.2 4.9 - - + +
156A GLN* 1.3 75.6 - - - +
158A LEU* 1.3 63.4 + - - +
1C NAG 5.8 0.5 - - - +
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Residues in contact with LEU 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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16A ILE* 3.7 13.5 - - + -
17A VAL 4.2 2.2 - - - +
18A GLY 3.4 26.9 - - - +
19A GLY* 3.6 6.1 - - - -
20A ARG* 4.6 2.9 - - - +
137A LEU* 3.4 5.7 - - - +
138A ALA* 2.9 40.8 + - + +
157A GLU* 1.3 77.6 - - - +
159A ASN* 1.3 72.2 + - + +
160A VAL* 3.4 22.2 + - + +
185A VAL* 4.0 5.2 - - + -
187A ARG* 3.5 16.4 - - - +
188A ALA* 4.2 4.5 - - + -
189A GLY* 3.7 37.0 - - - +
190A VAL* 5.9 0.2 - - + -
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Residues in contact with ASN 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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20A ARG* 2.9 35.0 + - - +
135A GLN* 5.4 5.2 - - - +
136A CYS 3.6 7.5 + - - -
137A LEU* 3.6 3.4 - - - +
158A LEU* 1.3 78.3 - - + +
160A VAL* 1.3 64.4 + - - +
185A VAL* 3.7 9.9 - - - +
187A ARG* 5.4 1.0 + - - -
1C NAG 1.4 75.0 + - + +
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Residues in contact with VAL 160 (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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135A GLN* 3.8 7.1 + - - -
136A CYS* 2.9 42.4 + - + +
138A ALA* 4.0 13.2 - - + +
158A LEU* 3.5 29.6 - - + +
159A ASN* 1.3 79.3 - - - +
162A THR* 1.4 66.0 + - - +
183A THR* 3.8 22.4 - - + +
184A LEU* 4.5 5.2 - - - +
185A VAL* 3.9 10.1 - - + +
189A GLY* 5.6 1.3 - - - -
190A VAL* 6.5 0.2 - - + -
199A LEU* 3.7 29.2 - - + -
226A ASP* 5.8 1.8 - - - +
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Residues in contact with THR 162 (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 GLY* 3.7 24.9 - - - +
134A VAL 3.6 5.8 - - - +
135A GLN* 3.7 17.3 + - - +
160A VAL* 1.4 79.2 + - - +
163A VAL* 1.3 67.5 + - - +
164A VAL* 3.4 3.5 - - - +
183A THR* 3.2 4.2 - - - -
184A LEU 2.9 37.9 + - - -
186A ARG* 3.6 36.4 + - - +
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Residues in contact with VAL 163 (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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130A LEU* 4.3 22.0 - - + +
131A GLY 3.8 24.5 - - - +
132A ASN* 2.8 4.0 + - - +
133A GLY 2.8 27.0 + - - -
134A VAL* 3.0 17.4 + - + +
136A CYS* 3.5 29.6 - - - -
162A THR* 1.3 73.4 - - - +
164A VAL* 1.3 68.6 + - - +
165A THR* 5.4 2.2 - - + -
181A VAL* 4.3 20.2 - - + -
182A CYS 3.3 13.9 - - - +
183A THR* 4.3 4.5 - - + +
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Residues in contact with VAL 164 (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 ASN* 3.1 15.0 - - - +
162A THR* 3.4 11.2 - - - +
163A VAL* 1.3 83.8 - - - +
165A THR* 1.3 67.6 + - - +
166A SER* 4.0 16.6 - - - +
168A CYS* 3.9 4.0 - - - +
182A CYS* 2.8 29.6 + - + +
183A THR 4.3 1.1 - - - -
184A LEU* 4.0 17.5 - - + -
186A ARG* 4.1 22.7 - - - +
225A PRO* 3.7 30.7 - - + -
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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