Contacts of the strand formed by residues 190 - 197 (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 SER 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D LYS 3.8 0.4 - - - +
149D ILE* 3.5 4.7 - - - +
150D ASP* 2.7 50.4 + - - +
151D GLY 5.1 1.3 + - - -
189D ASN* 1.3 73.7 - - - +
191D TYR* 1.3 64.8 + - - +
192D THR* 3.9 8.8 - - - +
207D SER* 3.7 11.1 + - - -
208D PHE 3.6 4.3 - - - -
209D ASN* 3.5 17.4 + - - -
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Residues in contact with TYR 191 (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* 3.6 8.4 - - + +
131D VAL* 4.6 13.2 - - + -
147D TRP* 5.3 2.2 - + + -
148D LYS 3.5 2.2 - - - -
149D ILE* 3.6 31.9 - - + +
178D LEU* 4.8 5.6 - - + -
180D LEU* 4.0 16.0 - - + +
184D GLU 3.7 4.7 + - - -
185D TYR* 2.7 65.6 + + - -
188D HIS* 4.0 24.8 - - + +
189D ASN 3.9 8.5 - - - -
190D SER* 1.3 75.1 + - - +
192D THR* 1.3 61.7 + - - +
207D SER* 3.1 1.7 + - - -
208D PHE* 2.8 65.8 + + + -
210D ARG* 4.6 1.1 - - - -
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Residues in contact with THR 192 (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* 4.3 0.7 - - - -
146D LYS 3.8 0.2 - - - +
147D TRP* 3.5 10.9 - - - -
148D LYS* 2.8 64.5 + - + +
151D GLY* 5.6 4.5 - - - +
190D SER* 3.9 12.3 - - - +
191D TYR* 1.3 75.1 - - - +
193D CYS* 1.3 61.7 + - - +
194D GLU* 5.2 1.9 + - - +
205D VAL* 4.3 13.1 - - + +
206D LYS 3.4 3.8 - - - -
207D SER* 2.9 30.1 - - - +
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Residues in contact with CYS 193 (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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114D VAL* 4.6 4.4 - - - +
116D ILE* 4.0 10.3 - - + +
133D CYS* 2.0 54.1 - - + -
135D LEU* 4.6 4.3 - - - -
145D VAL* 4.2 18.4 - - - -
146D LYS 3.7 3.4 - - - -
147D TRP* 4.1 8.5 - - + -
192D THR* 1.3 74.0 - - - +
194D GLU* 1.3 63.8 + - - +
195D ALA 4.3 0.7 - - - -
204D ILE 3.8 1.0 - - - +
205D VAL* 3.3 3.6 - - - +
206D LYS 2.7 38.6 + - - +
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Residues in contact with GLU 194 (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* 3.7 1.7 - - - +
145D VAL* 3.4 5.7 - - - -
146D LYS* 2.8 75.7 + - + +
148D LYS* 3.4 29.5 + - + +
192D THR* 5.2 3.1 - - - +
193D CYS* 1.3 76.5 - - - +
195D ALA* 1.3 62.2 + - - +
196D THR* 4.1 2.5 + - - +
203D PRO* 3.7 31.0 - - + +
204D ILE 3.4 3.6 - - - +
205D VAL* 4.3 17.1 - - + +
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Residues in contact with ALA 195 (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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112D PRO* 4.6 7.6 - - + -
114D VAL* 4.3 15.7 - - + -
135D LEU* 3.5 31.4 - - + -
143D ILE* 4.7 2.2 - - + -
144D ASN 3.3 4.7 - - - +
145D VAL* 4.6 0.2 - - - +
193D CYS* 4.3 0.6 - - - -
194D GLU* 1.3 73.5 - - - +
196D THR* 1.3 62.9 + - - +
197D HIS* 4.0 2.0 + - - -
203D PRO* 3.3 3.8 - - - +
204D ILE* 2.6 47.9 + - + +
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Residues in contact with THR 196 (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* 3.5 5.4 - - - +
144D ASN* 2.8 51.9 + - + +
146D LYS* 5.6 2.9 - - - +
194D GLU* 4.1 3.7 + - - +
195D ALA* 1.3 72.2 + - - +
197D HIS* 1.3 65.8 + - - +
200D SER 5.4 3.1 - - - +
201D THR 5.8 3.1 - - - +
203D PRO* 3.9 22.0 - - + +
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Residues in contact with HIS 197 (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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110D ALA 3.3 14.3 + - - -
112D PRO* 3.9 19.4 - - + +
138D PHE* 3.6 4.1 - + - -
139D TYR 3.2 27.8 - - - -
140D PRO* 2.8 31.0 + - + +
142D ASP 3.0 26.1 + - - -
143D ILE* 3.9 17.9 - - + -
195D ALA 4.0 3.0 + - - +
196D THR* 1.3 78.8 - - - +
198D LYS* 1.3 63.2 + - - +
199D THR* 3.0 32.4 + - + +
200D SER* 2.8 26.8 + - - +
203D PRO* 5.9 0.2 - - - +
204D ILE* 6.1 1.8 - - + -
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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