Contacts of the strand formed by residues 193 - 198 (chain D) in PDB entry 4YHP
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 TYR 193 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ILE* 3.4 6.5 - - + +
133D VAL* 4.6 9.4 - - + -
149D TRP* 5.1 1.8 - + + -
150D LYS 3.8 1.6 - - - -
151D VAL* 3.5 37.0 - - + -
180D LEU* 4.3 10.1 - - + -
182D LEU* 3.9 17.8 - - + +
186D ASP 4.0 0.5 + - - -
187D TYR* 2.3 60.6 + + - -
190D HIS* 3.6 7.8 - - + +
191D LYS 3.9 17.3 - - - -
192D VAL* 1.3 72.3 - - - +
194D ALA* 1.3 59.7 + - - +
209D SER* 3.1 5.3 - - - -
210D PHE* 3.1 69.0 + + + -
211D ASN 4.6 0.7 - - - -
212D ARG* 4.0 8.7 - - - -
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Residues in contact with ALA 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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118D ILE* 4.2 0.2 - - - -
148D GLN 3.6 1.2 - - - +
149D TRP* 3.6 12.6 - - - -
150D LYS* 2.9 55.0 + - + +
192D VAL* 4.8 8.1 - - + -
193D TYR* 1.3 73.3 - - - +
195D CYS* 1.3 59.4 + - - +
196D GLU* 5.3 0.7 - - + +
207D THR* 4.0 14.8 - - + -
208D LYS 3.5 4.0 - - - -
209D SER* 3.9 13.2 - - - -
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Residues in contact with CYS 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D VAL* 4.6 0.2 - - - -
118D ILE* 3.7 11.9 - - + +
135D CYS* 2.0 54.5 - - + -
147D VAL* 3.6 23.8 - - - -
148D GLN 3.9 2.5 - - - -
149D TRP* 4.6 7.4 - - + -
194D ALA* 1.3 73.2 - - - +
196D GLU* 1.3 58.2 + - - +
197D VAL* 4.0 8.8 + - - +
206D VAL 3.7 1.0 - - - +
207D THR* 3.2 6.0 - - - +
208D LYS* 2.8 39.8 + - + +
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Residues in contact with GLU 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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146D LYS* 3.4 8.5 + - - +
147D VAL* 3.4 2.1 - - - -
148D GLN* 2.9 67.5 + - + +
150D LYS* 2.3 42.4 + - + +
194D ALA* 3.9 0.9 + - + +
195D CYS* 1.3 74.0 - - - +
197D VAL* 1.3 63.6 + - - +
198D THR* 4.3 8.9 + - - +
205D PRO* 4.4 20.5 - - + +
206D VAL 3.4 5.2 - - - +
207D THR* 3.6 16.5 + - + +
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D PRO* 4.1 17.9 - - + -
116D VAL* 3.5 36.3 - - + -
137D LEU* 3.6 39.5 - - + -
145D ALA* 5.5 0.2 - - + -
146D LYS 3.6 4.0 - - - +
147D VAL* 4.7 1.3 - - + -
195D CYS* 4.0 8.1 - - - -
196D GLU* 1.3 76.6 - - - +
198D THR* 1.3 68.5 + - - +
199D HIS* 4.1 2.0 - - + -
202D LEU* 3.8 11.8 - - + +
205D PRO* 3.3 5.1 - - - +
206D VAL 2.6 42.8 + - - +
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Residues in contact with THR 198 (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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145D ALA* 3.9 3.1 - - - +
146D LYS* 2.9 61.1 + - + +
196D GLU* 4.0 10.1 + - - +
197D VAL* 1.3 71.0 - - - +
199D HIS* 1.3 66.0 - - - +
205D PRO* 3.4 30.0 - - + +
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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