Contacts of the strand formed by residues 149 - 154 (chain D) in PDB entry 4PRH
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 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D GLN* 4.3 16.9 + - - -
140D LEU 2.6 21.7 + - - -
141D ARG* 3.6 12.8 - - - +
146D SER 5.2 1.5 + - - -
147D ASP 4.1 3.0 + - - -
148D LYS* 1.3 76.3 + - - +
150D VAL* 1.3 64.8 + - - +
151D CYS* 5.9 1.1 - - - -
193D TRP* 3.7 17.5 - - - +
194D SER 4.7 4.3 + - - +
199D PHE* 5.2 4.0 - - - -
138E PHE* 3.8 5.5 - - - -
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Residues in contact with VAL 150 (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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139D GLN* 3.7 4.3 - - - +
140D LEU* 2.9 54.1 + - + +
149D SER* 1.3 78.1 - - - +
151D CYS* 1.3 63.2 + - - +
152D LEU* 5.6 0.2 - - + -
191D VAL* 4.3 8.5 - - + -
192D ALA 3.6 7.0 - - - +
193D TRP* 3.8 9.0 - - + +
138E PHE* 3.8 23.1 - - + -
154E VAL* 4.1 17.9 - - + -
156E LEU* 3.8 39.3 - - + -
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Residues in contact with CYS 151 (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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137D VAL* 4.6 0.2 - - + -
138D TYR 3.4 5.6 - - - -
139D GLN* 4.9 3.6 - - - -
149D SER* 5.6 0.9 - - - -
150D VAL* 1.3 76.6 - - - +
152D LEU* 1.3 59.4 + - - +
191D VAL* 3.5 3.5 - - - +
192D ALA 2.8 36.3 + - - +
199D PHE* 3.7 27.6 - - - -
200D ALA* 4.0 1.3 - - - -
201D CYS* 3.3 41.5 - - - -
204D ALA* 3.8 16.8 - - + -
205D PHE* 3.8 8.6 - - + -
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Residues in contact with LEU 152 (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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136D ALA 3.6 1.6 - - - +
137D VAL* 3.4 2.3 - - - -
138D TYR* 2.8 44.5 + - + +
140D LEU* 3.7 25.1 - - + -
150D VAL* 4.2 0.4 - - + -
151D CYS* 1.3 72.1 - - - +
153D PHE* 1.3 59.2 + - - +
154D THR* 3.8 22.2 + - + -
189D SER* 3.2 26.7 - - - +
190D ALA 3.6 4.7 - - - +
191D VAL* 4.1 22.0 - - + +
205D PHE* 4.1 3.3 - - - -
144E GLU* 4.9 0.2 - - - +
152E THR* 3.3 29.8 - - + +
154E VAL* 4.3 10.3 - - + -
203E ARG* 4.4 5.2 - - + -
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Residues in contact with PHE 153 (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 PRO* 4.1 11.4 - - + -
136D ALA 3.6 10.5 - - - -
137D VAL* 3.7 12.1 - - + -
152D LEU* 1.3 70.9 - - - +
154D THR* 1.3 62.8 + - - +
156D PHE* 3.5 34.8 - + + -
160D THR* 3.8 13.9 - - + -
162D VAL* 4.1 14.8 - - + -
189D SER* 3.2 6.4 + - - -
190D ALA* 2.9 33.4 + - + +
205D PHE* 3.6 36.3 - + + -
208D SER* 5.6 3.1 - - - -
210D ILE* 3.8 26.2 - - + -
211D PRO* 3.9 16.8 - - + -
214D THR* 4.1 19.5 - - + -
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Residues in contact with THR 154 (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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134D ASP 3.8 0.2 - - - +
135D PRO* 3.5 0.9 - - - +
136D ALA 3.0 34.0 + - - +
138D TYR* 3.5 39.5 - - + -
152D LEU* 3.8 12.8 - - + -
153D PHE* 1.3 76.1 - - - +
155D ASP* 1.4 86.9 + - + +
156D PHE* 3.3 7.1 + - - -
187D SER* 3.8 0.5 + - - -
188D ASN 3.2 12.0 + - - -
189D SER* 3.4 13.3 + - - -
144E GLU* 5.2 0.7 - - - +
152E THR* 5.2 2.0 - - - +
205E ARG* 3.7 13.7 + - - +
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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