Contacts of the strand formed by residues 153 - 164 (chain B) in PDB entry 3K3B
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 GLU 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B THR* 1.3 69.4 - - - +
154B PHE* 1.3 61.0 + - - +
244B HIS 3.7 0.7 - - - +
245B MET* 3.4 1.6 - - - -
246B LYS* 2.7 65.1 + - + +
248B THR* 5.4 2.3 + - - -
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Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE 4.2 8.3 - - - -
144B PHE* 3.7 33.2 - + - -
147B LEU* 3.8 48.2 - - + -
148B THR* 3.8 18.8 - - - -
152B THR* 3.2 18.6 - - + -
153B GLU* 1.3 78.0 - - - +
155B SER* 1.3 62.6 - - - +
156B VAL* 3.8 22.7 - - + -
243B ILE* 4.2 1.1 - - + -
244B HIS 2.9 13.7 - - - +
245B MET* 4.2 4.7 - - + -
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Residues in contact with SER 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B PHE* 1.3 77.7 - - - +
156B VAL* 1.3 63.4 + - - +
157B LYS* 6.0 0.4 - - - -
203B THR* 5.2 10.1 - - - -
242B THR 3.5 1.9 - - - +
243B ILE* 3.4 6.1 - - - +
244B HIS* 3.0 50.1 + - - +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 4.5 9.9 - - + -
143B ILE* 3.8 20.2 - - + -
144B PHE* 3.8 18.8 - - + -
154B PHE* 3.8 22.4 - - + -
155B SER* 1.3 77.8 - - - +
157B LYS* 1.3 56.8 + - - +
158B VAL* 4.6 0.7 - - + -
203B THR* 3.4 7.2 - - - +
204B VAL* 2.6 55.3 + - + +
241B VAL* 3.5 31.6 - - + -
242B THR 3.6 2.7 - - - +
243B ILE* 4.6 3.4 - - + -
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Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B SER 4.2 0.6 - - - +
156B VAL* 1.3 74.2 - - - +
158B VAL* 1.3 63.6 + - - +
201B GLU* 3.1 42.5 + - + +
202B ILE 3.0 17.5 - - - +
203B THR* 4.1 9.6 - - + +
240B SER 4.0 0.2 - - - +
241B VAL* 3.5 1.9 - - - +
242B THR* 2.8 51.2 + - - +
244B HIS* 3.9 30.0 - - - +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.9 20.4 - - + -
156B VAL* 4.6 0.4 - - + -
157B LYS* 1.3 79.1 - - - +
159B SER* 1.3 60.9 + - - +
172B LEU* 3.8 11.1 - - + +
201B GLU* 3.4 4.7 - - - -
202B ILE* 2.8 34.1 + - + +
204B VAL* 3.9 23.6 - - + -
213B ILE* 3.9 23.6 - - + -
239B PHE* 3.8 30.1 - - + -
240B SER 3.1 11.4 - - - +
241B VAL* 3.9 6.1 - - + -
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B VAL* 1.3 75.0 - - - +
160B LEU* 1.3 62.0 + - - +
161B LEU* 4.3 0.6 - - - +
172B LEU* 3.7 5.4 - - - -
199B LEU* 3.9 23.4 - - - +
200B GLU 3.4 20.0 - - - -
201B GLU* 3.6 16.5 + - - -
238B VAL 4.3 1.0 + - - -
239B PHE* 3.5 5.4 - - - -
240B SER* 2.9 46.9 + - - +
260B LYS* 5.1 1.4 + - - -
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B SER* 1.3 75.9 - - - +
161B LEU* 1.3 61.9 + - - +
170B ASP* 3.6 6.7 + - - +
171B LEU* 2.9 46.5 + - + -
172B LEU* 3.4 22.2 + - + +
199B LEU* 4.9 1.3 - - - -
200B GLU 4.8 0.6 + - - -
217B GLY* 3.8 23.6 - - - -
221B ARG* 4.4 2.5 - - - +
237B SER* 3.3 27.4 - - - +
238B VAL 3.5 10.5 - - - +
239B PHE* 3.9 22.2 - - + -
372B L31 3.2 30.7 - - + -
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B SER* 4.3 0.9 - - - +
160B LEU* 1.3 75.0 - - - +
162B GLU* 1.3 64.3 + - - +
163B ILE* 3.6 31.0 - - + -
168B LEU* 4.2 11.9 - - + -
169B PHE 3.1 13.9 - - - +
171B LEU* 4.5 4.5 - - - -
182B LEU* 4.8 2.0 - - + -
196B ILE* 3.6 35.7 - - + -
199B LEU* 4.0 25.6 - - + -
236B HIS 4.0 0.2 - - - +
237B SER* 3.6 3.5 + - - -
238B VAL* 2.9 49.7 + - + +
319B ILE* 4.4 9.6 - - + -
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 1.3 73.2 - - - +
163B ILE* 1.3 62.9 + - - +
164B TYR* 4.6 2.0 - - + +
167B GLU 3.2 4.5 - - - +
168B LEU* 3.4 0.7 - - - -
169B PHE* 2.7 48.2 + - + +
171B LEU* 3.9 17.1 - - + +
221B ARG* 3.3 32.6 - - - +
224B ALA* 4.0 14.0 - - - +
230B ALA* 3.9 23.6 - - - +
232B SER* 4.0 5.0 - - - -
235B SER* 2.8 33.9 + - - +
236B HIS 3.3 10.8 - - - +
237B SER* 5.1 2.2 - - - -
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 3.6 19.3 - - + -
162B GLU* 1.3 69.8 - - - +
164B TYR* 1.3 60.9 + - - +
165B ASN 4.2 1.3 + - - +
166B GLU* 4.3 2.5 - - - +
167B GLU 3.3 13.2 - - - +
168B LEU* 3.8 13.9 - - + -
235B SER* 3.3 5.3 - - - -
236B HIS* 2.9 45.4 + - + +
238B VAL* 4.3 5.8 - - + -
288B ILE* 4.6 1.9 - - + +
315B LYS* 4.8 0.2 - - + -
316B LEU* 3.7 47.1 - - + +
319B ILE* 4.0 14.8 - - + -
369B NO3 3.4 28.3 - - - +
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Residues in contact with TYR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLY 5.1 0.3 + - - -
56A GLY* 3.8 17.3 + - - -
57A LEU* 3.5 41.3 - - + -
162B GLU* 3.6 3.2 + - + -
163B ILE* 1.3 72.3 - - - +
165B ASN* 1.3 78.6 + - + +
166B GLU 3.4 0.9 - - - -
167B GLU* 2.9 26.5 + - - +
169B PHE* 4.1 10.5 - + + -
229B ASN 3.0 26.5 + - - -
230B ALA* 3.6 30.5 - - + -
231B TYR* 3.9 6.9 - - - -
234B ARG* 4.1 29.0 - - + -
235B SER* 3.9 18.8 - - - +
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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