Contacts of the strand formed by residues 143 - 149 (chain D) in PDB entry 4WFH
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 ILE 143 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D PRO* 3.9 22.9 - - + -
135D LEU* 3.6 25.1 - - + -
138D PHE* 3.8 25.4 - - + -
141D LYS 3.1 13.7 + - - +
142D ASP* 1.3 75.4 - - - +
144D ASN* 1.3 71.1 + - - +
162D TRP* 4.2 11.4 + - - +
174D MET* 4.2 22.2 - - - +
195D ALA* 4.7 0.9 - - + -
196D THR 3.5 15.7 - - - +
197D HIS* 3.9 15.5 - - + -
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Residues in contact with ASN 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ILE* 1.3 76.4 - - - +
145D VAL* 1.3 76.3 + - - +
146D LYS* 3.6 27.1 + - - +
194D GLU 4.5 0.7 - - - +
195D ALA* 3.3 3.8 - - - -
196D THR* 2.8 56.9 + - + +
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 3.3 42.4 - - + -
143D ILE* 5.3 0.7 - - + -
144D ASN* 1.3 82.8 + - - +
146D LYS* 1.3 79.3 + - - +
147D TRP* 4.3 7.1 - - + +
160D ASN* 5.1 6.1 + - - +
174D MET* 4.1 20.6 - - + -
176D SER* 4.0 24.5 - - - +
193D CYS* 4.2 13.9 - - - -
194D GLU 3.4 5.8 - - - +
195D ALA* 4.9 0.4 - - + -
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D ASN* 3.6 22.9 - - - +
145D VAL* 1.3 77.5 - - - +
147D TRP* 1.3 65.0 + - - +
148D LYS* 4.3 15.0 - - - +
153D GLU* 3.3 40.5 + - - +
192D THR 3.8 0.3 - - - +
193D CYS* 3.7 2.6 - - - -
194D GLU* 2.8 71.1 + - + +
196D THR* 5.6 3.1 - - - +
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Residues in contact with TRP 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ILE* 3.8 17.3 - - + -
131D VAL* 3.5 46.9 - - + -
132D VAL 4.0 1.3 - - - -
133D CYS* 3.7 22.7 - - + -
145D VAL* 4.3 6.2 - - + +
146D LYS* 1.3 77.6 - - - +
148D LYS* 1.3 64.2 - - - +
153D GLU* 3.2 10.2 - - - +
154D ARG* 2.9 41.4 + - + +
158D VAL* 3.6 29.1 - - + +
176D SER* 3.1 42.9 + - - -
178D LEU* 3.9 30.7 - - + +
191D TYR* 5.3 2.7 - + + -
192D THR 3.5 18.4 - - - -
193D CYS* 4.1 7.4 - - + -
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Residues in contact with LYS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS* 4.3 21.5 - - - +
147D TRP* 1.3 81.8 - - - +
149D ILE* 1.3 63.2 + - - +
150D ASP 4.1 0.4 - - - -
151D GLY* 3.7 31.8 + - - +
152D SER 3.2 4.9 - - - +
153D GLU* 3.9 13.2 - - + -
190D SER 3.8 0.7 - - - +
191D TYR* 3.5 5.0 - - - -
192D THR* 2.8 57.3 + - + +
194D GLU* 3.4 34.5 + - + +
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Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LYS* 1.3 74.7 - - - +
150D ASP* 1.3 71.7 + - - +
151D GLY 3.1 0.2 - - - -
152D SER* 2.6 29.8 + - - +
154D ARG* 3.7 47.3 - - + +
178D LEU* 4.2 14.1 - - + -
180D LEU* 4.5 5.8 - - + -
188D HIS* 3.3 47.6 + - + +
190D SER 3.5 3.4 - - - +
191D TYR* 3.6 29.4 - - + +
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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