Contacts of the strand formed by residues 149 - 158 (chain D) in PDB entry 3C8J
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 LYS 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D CYS* 3.3 3.6 - - - +
146D TYR 2.8 30.0 + - - +
147D SER* 3.4 1.0 + - - -
148D THR* 1.3 86.7 - - - +
150D CYS* 1.3 63.9 + - - +
151D TYR* 3.5 20.9 - - + +
175D LEU* 4.2 4.8 - - - +
176D LYS* 2.8 25.7 + - - +
178D GLU* 2.9 21.2 + - - +
182D GLU* 2.8 32.0 + - - +
254D GLY 4.6 1.4 - - - -
255D LYS* 3.2 23.7 - - - +
256D LYS* 3.7 30.5 - - + +
257D LEU* 4.5 0.2 - - - -
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Residues in contact with CYS 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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260C PHE* 3.6 31.0 - - + -
261C PRO* 3.5 20.9 - - + -
143D TRP* 4.6 0.7 - - + -
144D PHE 3.6 5.6 - - - +
145D CYS* 2.0 47.3 - - - -
149D LYS* 1.3 74.9 - - - +
151D TYR* 1.3 64.0 + - - +
254D GLY* 3.4 2.9 - - - -
255D LYS 3.1 29.6 + - - +
257D LEU* 4.0 13.9 - - + -
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Residues in contact with TYR 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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260C PHE* 4.3 0.9 - - - -
143D TRP* 3.1 6.2 - - - -
144D PHE 2.9 41.2 + - - +
146D TYR* 4.2 8.8 + - + +
149D LYS* 3.5 36.2 - - + +
150D CYS* 1.3 76.4 - - - +
152D TYR* 1.3 60.3 + - - +
153D PHE* 3.4 24.7 - + + -
175D LEU* 3.5 25.4 - - + -
182D GLU* 2.5 45.2 + - + +
185D PHE* 3.8 24.0 - + - -
186D LEU* 3.7 18.8 - - + -
252D ILE* 4.3 2.0 - - + -
253D CYS 3.2 12.1 - - - +
254D GLY* 4.1 3.4 - - - -
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Residues in contact with TYR 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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260C PHE* 3.2 56.2 - + + +
141D LYS* 5.3 1.6 - - + -
142D TYR* 3.2 25.8 - - - -
143D TRP* 4.2 15.9 + + + +
150D CYS 4.4 0.6 + - - -
151D TYR* 1.3 70.4 - - - +
153D PHE* 1.3 62.5 + - - +
154D ILE* 3.9 3.7 + - + -
170D TYR* 3.5 69.3 + + + -
172D VAL* 4.5 6.1 - - + -
251D CYS 3.9 0.3 - - - +
252D ILE* 3.6 4.0 - - - +
253D CYS* 2.9 49.9 + - + +
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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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141D LYS* 3.3 7.4 - - - +
142D TYR* 3.0 66.8 + + + +
144D PHE* 4.4 5.2 - + + -
151D TYR* 3.4 31.9 - + + -
152D TYR* 1.3 71.2 - - - +
154D ILE* 1.3 60.8 + - - +
155D MET* 3.9 9.6 + - + +
186D LEU* 3.8 21.8 - - + -
189D HIS* 3.3 28.3 - + - -
190D VAL* 3.2 34.8 - - + -
195D TYR* 4.4 4.5 - + + -
251D CYS 3.9 1.1 - - - -
252D ILE* 3.7 27.1 - - + -
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Residues in contact with ILE 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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138D ARG* 5.1 1.6 - - - +
141D LYS* 4.2 18.6 - - + -
152D TYR* 4.4 7.9 - - + +
153D PHE* 1.3 75.1 - - - +
155D MET* 1.3 62.4 + - - +
156D ASN* 3.2 21.0 + - + +
166D ASN* 3.8 39.9 - - + +
170D TYR* 3.6 30.7 - - + -
195D TYR* 4.8 1.2 - - - -
250D TYR* 3.3 5.2 - - - +
251D CYS* 2.8 49.5 + - + +
253D CYS* 3.8 19.7 - - - -
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Residues in contact with MET 155 (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 GLY* 3.4 16.6 - - - -
140D VAL* 2.9 39.3 + - + +
142D TYR* 4.1 20.6 - - + +
153D PHE* 4.2 11.4 - - + +
154D ILE* 1.3 73.3 - - - +
156D ASN* 1.3 59.1 + - - +
191D ILE* 4.0 28.5 - - + -
195D TYR* 3.2 36.3 - - - +
250D TYR* 3.5 33.5 - - + -
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Residues in contact with ASN 156 (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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138D ARG* 3.0 51.7 - - - +
139D GLY 2.9 22.4 + - - +
141D LYS* 3.6 15.8 - - - +
154D ILE* 3.2 15.1 + - + +
155D MET* 1.3 76.5 - - - +
157D LYS* 1.3 67.6 + - - +
158D THR* 3.3 8.5 + - + +
166D ASN* 4.7 7.8 + - - +
249D TYR 3.2 9.2 - - - +
250D TYR* 3.6 10.4 - - - -
251D CYS* 4.4 1.0 + - - +
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Residues in contact with LYS 157 (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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156D ASN* 1.3 73.7 + - - +
158D THR* 1.3 62.9 + - - +
248D PRO* 3.9 35.7 - - + +
249D TYR* 3.1 10.5 - - - +
250D TYR* 3.7 36.1 + - + -
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Residues in contact with THR 158 (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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156D ASN* 3.3 9.5 + - + +
157D LYS* 1.3 79.1 - - - +
159D THR* 1.3 71.7 + - - +
162D GLY* 4.0 7.9 - - - -
163D CYS* 3.2 23.1 + - - +
166D ASN* 3.7 25.0 + - - +
196D TRP* 2.9 21.3 + - - -
248D PRO* 3.1 10.2 - - - +
249D TYR 2.8 18.5 + - - -
251D CYS* 4.6 0.7 - - - +
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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