Contacts of the strand formed by residues 189 - 197 (chain A) in PDB entry 2WFK
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 GLY 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A TRP* 3.4 18.2 - - - -
67A ILE 2.9 31.1 + - - -
120A ARG* 6.2 1.6 - - - -
123A ALA 3.6 9.6 - - - -
124A ILE* 4.6 2.9 - - - -
187A VAL 3.3 1.5 + - - -
188A ARG* 1.3 78.2 - - - +
190A LEU* 1.3 59.5 + - - -
191A TYR* 3.4 14.4 - - - -
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Residues in contact with LEU 190 (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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64A TYR* 4.1 14.6 - - + -
65A VAL 3.4 15.7 - - - +
66A TRP* 4.1 5.6 - - + +
120A ARG* 3.8 3.3 - - - +
121A MSE 2.8 51.4 + - + +
123A ALA* 3.4 24.6 + - + +
129A ILE* 3.8 34.8 - - + +
132A ALA* 4.0 10.3 - - + -
133A ALA 4.3 3.8 - - - +
189A GLY* 1.3 70.3 - - - -
191A TYR* 1.3 74.3 + - - +
233A LEU* 3.8 25.8 - - + -
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Residues in contact with TYR 191 (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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63A LEU 3.9 0.3 - - - +
64A TYR* 3.4 4.5 - - - +
65A VAL* 2.8 47.8 + - + +
67A ILE* 3.6 19.1 - - + -
74A MSE 4.5 9.4 - - + -
118A VAL* 4.9 6.1 - - + -
119A GLU 3.3 10.5 - - - +
120A ARG* 2.9 37.7 + - + -
121A MSE 4.3 2.7 - - - +
141A LEU* 3.6 34.1 - - + -
186A LEU* 3.3 16.1 - - + -
187A VAL 2.7 35.1 + - - -
188A ARG 4.5 0.2 + - - -
189A GLY* 3.4 23.3 - - - -
190A LEU* 1.3 78.4 - - - +
192A ARG* 1.3 62.1 + - - +
193A ILE* 5.6 0.7 - - + -
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Residues in contact with ARG 192 (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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62A TYR* 3.5 56.9 + - + -
63A LEU 3.6 2.7 - - - +
64A TYR* 3.7 29.3 + - + -
117A ARG 3.8 1.0 - - - +
118A VAL* 3.7 1.9 - - - -
119A GLU* 2.8 63.1 + - + +
121A MSE 3.8 36.1 - - + +
133A ALA 4.4 8.5 + - - -
135A ALA 4.9 1.4 + - - -
137A PRO* 3.2 24.4 - - - +
191A TYR* 1.3 74.5 - - - +
193A ILE* 1.3 65.3 + - - +
194A SER* 3.9 1.6 + - - -
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Residues in contact with ILE 193 (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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61A TYR 3.6 1.4 - - - +
62A TYR* 3.3 8.7 - - - -
63A LEU* 2.9 36.8 + - + +
65A VAL* 3.9 24.5 - - + -
74A MSE 4.2 9.2 - - - -
76A VAL* 3.7 25.1 - - + -
116A ILE* 4.1 5.4 - - + -
117A ARG 3.5 9.2 - - - +
118A VAL* 4.5 10.8 - - + +
191A TYR* 5.3 1.1 - - + -
192A ARG* 1.3 77.4 - - - +
194A SER* 1.3 61.2 + - - +
195A PHE* 3.6 29.4 + - + -
211A VAL* 3.7 32.3 - - + -
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Residues in contact with SER 194 (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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54A VAL* 4.1 23.4 - - - +
60A ALA* 4.4 1.8 - - - -
61A TYR 3.8 3.4 - - - -
62A TYR* 3.1 28.6 - - - -
115A TRP 3.7 0.2 - - - +
116A ILE* 3.5 7.4 - - - +
117A ARG* 2.7 44.3 + - - -
119A GLU* 4.3 8.3 + - - -
192A ARG* 3.9 8.2 + - - +
193A ILE* 1.3 71.3 - - - +
195A PHE* 1.3 62.6 + - - +
196A THR* 3.6 2.6 + - - +
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Residues in contact with PHE 195 (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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40A TYR* 4.7 6.7 - + - -
60A ALA* 3.4 1.2 - - - -
61A TYR* 2.8 56.8 + - - +
63A LEU* 3.7 31.2 - - + -
76A VAL* 3.5 27.1 - - + -
77A ARG 3.7 7.2 - - - -
78A MSE 3.7 33.2 - - + -
116A ILE* 4.2 5.4 - - + -
193A ILE* 3.6 23.6 - - + -
194A SER* 1.3 71.2 - - - +
196A THR* 1.3 59.2 + - - +
207A PHE* 4.4 8.7 - - + -
209A ALA* 3.4 33.2 - - + -
210A SER 4.6 0.2 - - - -
211A VAL* 4.0 13.5 - - + -
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Residues in contact with THR 196 (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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54A VAL* 4.0 16.8 - - + +
58A LYS* 3.4 18.6 + - + +
59A LYS 2.6 22.3 + - - -
60A ALA* 4.0 11.0 - - - -
61A TYR* 5.6 0.2 - - - -
78A MSE 3.6 12.7 - - - +
112A PHE* 3.8 1.4 - - - -
114A THR 3.8 0.9 - - - -
115A TRP* 2.8 56.4 + - + +
117A ARG* 5.0 1.1 - - + +
194A SER* 4.1 7.2 - - - +
195A PHE* 1.3 76.5 - - - +
197A THR* 1.3 76.6 + - - +
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Residues in contact with THR 197 (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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44A VAL* 5.6 2.9 - - + -
58A LYS* 2.9 39.3 + - - +
59A LYS* 4.1 16.6 + - + +
61A TYR* 6.4 0.7 - - + -
112A PHE* 3.6 24.5 - - + -
113A ASP 3.5 8.5 - - - -
115A TRP* 3.5 6.4 - - - +
196A THR* 1.3 89.3 + - - +
198A TYR* 1.3 59.9 + - - +
199A LYS 2.6 28.3 + - - -
201A GLY 5.0 1.2 + - - -
203A VAL* 4.2 20.3 - - + +
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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