Contacts of the strand formed by residues 156 - 163 (chain A) in PDB entry 2W2R
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 GLU 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLY* 3.2 25.1 - - - -
98A MSE 3.2 37.0 + - + +
101A LYS* 4.2 0.6 - - + +
105A TYR* 2.6 33.2 + - + +
154A VAL* 3.9 6.3 + - + +
155A SER* 1.3 79.4 - - - +
157A THR* 1.3 62.8 - - - +
158A PHE* 3.8 18.7 - - + -
173A PHE 3.9 0.9 - - - +
174A THR* 3.4 1.8 - - - -
175A PHE* 2.9 31.5 + - - +
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Residues in contact with THR 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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155A SER* 5.1 1.4 + - - -
156A GLU* 1.3 72.9 - - - +
158A PHE* 1.3 75.4 + - - +
159A ARG* 3.7 42.0 + - + +
172A ASP* 3.9 11.4 - - - +
173A PHE 3.2 9.6 - - - +
174A THR* 2.9 25.5 + - - +
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Residues in contact with PHE 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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91A TRP* 3.8 32.8 - + + +
95A TYR* 3.7 34.1 - + - -
96A ILE* 5.2 5.2 - - + -
97A GLY* 4.3 13.2 - - - -
105A TYR* 4.0 9.9 - + - -
156A GLU* 3.8 37.5 - - + -
157A THR* 1.3 79.8 - - - +
159A ARG* 1.3 62.7 + - - +
160A LYS* 4.1 24.9 - - + +
171A LEU* 3.7 2.8 - - - +
172A ASP* 3.4 2.9 + - - -
173A PHE* 2.8 45.6 + - + +
175A PHE* 4.0 18.4 - + - -
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Residues in contact with ARG 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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157A THR* 3.7 27.0 + - + +
158A PHE* 1.3 77.6 - - - +
160A LYS* 1.3 72.5 + - - +
161A PRO* 4.7 0.7 - - - +
171A LEU 3.3 5.6 - - - +
172A ASP* 3.8 29.4 + - + +
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLN 4.8 2.5 - - - +
91A TRP* 3.0 37.9 + - + +
94A SER* 2.9 41.9 + - - +
95A TYR* 4.8 2.0 - - - +
96A ILE* 5.6 1.9 - - - +
158A PHE* 4.1 21.0 - - + +
159A ARG* 1.3 91.1 - - - +
161A PRO* 1.3 80.6 - - + +
170A THR* 3.4 5.9 - - - -
171A LEU* 2.8 42.1 + - + +
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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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90A GLN* 4.4 9.9 - - - +
159A ARG 4.7 0.2 - - - +
160A LYS* 1.3 100.2 - - + +
162A PHE* 1.3 64.6 + - - +
169A GLY 3.3 11.4 - - - +
170A THR* 4.3 6.3 - - + -
171A LEU* 4.6 1.4 - - - +
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Residues in contact with PHE 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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72A VAL* 3.8 15.0 - - + -
73A ARG 3.4 23.6 - - - -
74A SER* 4.1 3.8 - - - -
78A PHE* 3.9 18.8 - + - -
87A ALA* 3.6 38.6 - - + +
90A GLN* 3.9 12.3 - - + -
161A PRO* 1.3 76.9 - - - +
163A ASN* 1.3 64.6 + - - +
164A ILE* 4.5 3.6 - - + -
167A TYR* 3.7 13.9 - - + -
168A LYS* 3.3 35.6 - - - +
169A GLY 2.9 42.2 + - - +
170A THR 3.5 4.5 - - - -
171A LEU* 3.5 20.9 - - + -
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Residues in contact with ASN 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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90A GLN* 4.1 10.8 + - - +
162A PHE* 1.3 76.9 - - - +
164A ILE* 1.3 68.8 + - - +
165A GLY* 3.2 13.7 + - - +
167A TYR 3.7 7.4 - - - +
168A LYS* 3.8 31.6 - - + +
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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