Contacts of the strand formed by residues 152 - 158 (chain A) in PDB entry 2W7W
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 THR 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A VAL* 3.4 2.6 - - - -
128A LYS* 2.7 57.6 + - - -
150A GLY 4.1 4.9 + - - -
151A VAL* 1.3 74.5 - - - +
153A PRO* 1.4 78.6 - - + +
154A LEU* 3.4 3.6 + - + +
191A ASN 3.9 20.9 - - - +
194A LYS* 4.0 33.9 + - + +
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Residues in contact with PRO 153 (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 TRP* 3.9 19.7 - - + -
76A PHE* 3.5 28.2 - - + -
125A TRP* 4.0 16.6 - - + -
126A LEU 4.2 4.5 - - - +
127A VAL* 4.4 7.2 - - + -
145A PRO* 4.0 23.3 - - + +
146A LEU* 4.3 15.9 - - + +
151A VAL 3.7 9.6 - - - +
152A THR* 1.4 89.5 - - + +
154A LEU* 1.3 63.4 + - - +
191A ASN* 3.7 9.0 - - - +
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Residues in contact with LEU 154 (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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76A PHE* 3.7 6.5 - - - -
93A VAL* 6.4 0.2 - - + -
126A LEU* 2.9 37.4 + - + +
128A LYS* 3.9 16.8 - - + +
134A LEU* 4.2 15.7 - - + -
152A THR* 3.6 17.9 - - + +
153A PRO* 1.3 78.6 - - - +
155A LEU* 1.3 63.8 + - - +
187A PHE* 4.6 1.6 - - - -
188A VAL* 3.6 28.0 - - + +
191A ASN* 3.1 48.9 + - - +
192A LEU* 3.9 24.2 - - + +
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Residues in contact with LEU 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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76A PHE* 3.8 3.9 - - - -
80A CYS* 3.8 31.4 - - + +
107A PHE* 4.5 16.8 - - + -
111A PHE* 4.6 7.4 - - + -
125A TRP* 3.3 7.1 - - - +
126A LEU* 2.9 36.6 + - + +
154A LEU* 1.3 80.2 - - + +
156A THR* 1.3 63.1 + - - +
179A PHE* 3.9 25.4 - - + -
180A TRP* 4.8 2.5 - - + -
183A VAL* 3.8 21.8 - - + -
185A TRP* 4.2 26.9 - - + -
188A VAL* 3.8 12.6 - - + -
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Residues in contact with THR 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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73A ASN 4.6 0.2 - - - +
76A PHE* 3.7 20.4 - - + -
77A TYR* 3.9 30.4 - - + +
80A CYS* 3.6 9.1 - - - +
111A PHE* 4.6 1.1 - - - -
123A TRP* 3.7 17.9 - - + +
124A THR 3.1 13.9 + - - -
125A TRP* 3.3 35.3 - - + -
155A LEU* 1.3 77.4 - - - +
157A VAL* 1.3 62.3 + - - +
179A PHE* 3.3 20.2 - - - -
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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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77A TYR* 4.2 1.6 - - + -
111A PHE* 3.6 23.3 - - + -
115A ALA* 4.1 0.9 - - + -
123A TRP* 3.4 9.0 - - - -
124A THR* 2.9 40.4 + - - +
156A THR* 1.3 75.0 + - - +
158A ASP* 1.3 61.0 + - - +
159A LEU* 3.6 10.3 + - + +
175A TYR* 3.4 38.6 - - + +
176A MET* 4.0 15.5 - - + -
179A PHE* 3.7 27.4 - - + -
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Residues in contact with ASP 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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27A HIS* 2.8 8.7 + - - -
74A HIS* 3.2 4.0 + - - -
77A TYR* 3.6 21.7 - - + -
123A TRP* 3.4 29.0 - - + -
157A VAL* 1.3 71.0 - - - +
159A LEU* 1.3 63.1 + - - +
160A TRP* 3.2 26.4 + - - -
163A ALA* 3.5 17.5 - - + +
175A TYR* 2.5 32.2 + - - -
1195A FE 1.8 32.7 - - - -
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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