Contacts of the strand formed by residues 156 - 161 (chain A) in PDB entry 1D6W
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.7 20.5 + - + +
19A GLY* 4.0 7.5 + - - +
20A SER* 3.3 24.7 + - - +
21A ASP* 2.6 25.9 + - - +
22A ALA* 4.6 0.4 - - - -
139A THR* 3.3 11.1 - - - +
140A GLY 3.2 33.1 + - - +
144A LEU* 3.9 19.0 - - + +
152A PRO* 3.6 33.3 - - + +
154A VAL 2.8 15.1 - - - +
155A LEU* 1.3 73.5 - - - +
157A VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 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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14A THR* 5.3 5.2 - - - +
16A ILE* 4.0 2.5 - - - -
19A GLY* 3.0 6.1 - - - -
20A SER* 2.9 52.6 + - - +
21A ASP 4.2 0.7 - - - +
22A ALA* 3.9 19.3 - - - -
26A MET* 4.0 20.0 - - + -
137A ARG* 3.4 36.8 - - + +
138A VAL 3.4 4.5 - - - -
139A THR* 3.3 25.8 - - + -
156A GLN* 1.3 72.0 - - - +
158A VAL* 1.3 60.7 + - - +
159A ASN* 5.1 0.9 - - - +
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Residues in contact with VAL 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* 3.5 24.7 - - + -
18A GLU 4.1 11.2 - - - +
19A GLY* 4.2 1.3 - - - -
137A ARG* 3.4 2.4 - - - -
138A VAL* 2.9 41.9 + - + +
157A VAL* 1.3 76.2 - - - +
159A ASN* 1.3 68.8 + - - +
160A LEU* 3.6 40.4 + - + +
184A TYR* 5.5 0.2 - - + -
186A LYS* 5.7 3.1 - - - -
187A ARG 4.3 3.4 - - - +
188A GLY* 3.9 15.7 - - - -
189A ASP 4.3 8.5 - - - +
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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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14A GLU* 2.9 90.2 + - + +
135A LYS* 4.7 3.1 - - + -
136A GLY 3.1 3.8 - - - -
137A ARG* 3.0 34.3 + - - +
157A VAL* 4.8 0.8 - - - +
158A VAL* 1.3 76.3 + - - +
160A LEU* 1.3 66.1 + - - +
184A TYR* 3.2 19.3 + - - -
186A LYS* 4.6 2.3 - - - -
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Residues in contact with LEU 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 LYS* 3.3 6.0 - - - -
136A GLY* 2.8 28.9 + - - +
138A VAL* 3.9 20.2 - - + -
158A VAL* 3.6 34.5 - - + +
159A ASN* 1.3 84.3 - - - +
161A PRO* 1.3 68.5 - - + +
162A ILE 3.9 0.3 + - - -
183A ALA* 4.4 10.1 - - + +
184A GLY* 3.9 29.8 - - + +
188A GLY 3.4 22.0 - - - +
189A ASP* 4.3 13.2 - - - +
199A PHE* 4.0 7.4 - - + -
228A TYR* 3.9 12.3 - - + +
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Residues in contact with PRO 161 (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* 4.0 20.2 - - - +
134A TYR 3.5 6.7 - - - +
135A LYS* 3.7 11.2 - - + -
160A LEU* 1.3 86.4 - - + +
162A ILE* 1.3 68.2 + - - +
163A VAL* 5.5 0.2 - - + -
183A ALA* 3.3 4.2 - - - +
184A GLY* 3.1 82.2 + - + +
186A GLU* 4.3 9.4 - - - +
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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