Contacts of the strand formed by residues 143 - 152 (chain B) in PDB entry 5H8N
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 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A THR* 5.7 0.4 - - - -
17B PHE* 4.6 9.0 - - + -
67B PHE* 4.4 14.1 - - + -
141B PRO* 3.3 2.8 - - - +
142B PHE* 1.4 93.2 - - + +
144B TYR* 1.3 84.0 + - - +
145B GLN* 4.4 7.5 - - + +
227B ALA* 4.5 15.3 - - + +
250B GLY* 3.2 4.3 - - - -
251B PHE* 3.0 51.4 + - + +
273B HIS* 4.3 2.2 + - - -
282B ASP* 3.5 29.9 + - - +
286B VAL* 5.3 5.8 - - + -
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Residues in contact with TYR 144 (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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116A ILE* 5.8 0.2 - - - +
129A PRO* 3.6 15.9 - - + +
132A GLU* 3.6 38.4 - - + +
241A THR* 3.3 31.9 - - + +
242A THR* 3.3 43.0 + - - -
243A GLY 3.4 2.9 + - - -
302A 5YD 3.8 34.1 - + + -
140B LYS* 5.6 0.9 - - - +
141B PRO* 3.7 39.6 + - + +
143B LYS* 1.3 90.3 + - - +
145B GLN* 1.4 64.4 + - - +
249B SER 4.0 2.5 - - - -
250B GLY* 4.4 0.2 - - - -
270B LEU* 6.0 1.9 - - - +
273B HIS* 4.4 2.5 - + - -
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Residues in contact with GLN 145 (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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132A GLU* 5.1 2.8 + - - +
302A 5YD 4.6 1.6 - - - -
143B LYS* 4.4 7.9 - - + +
144B TYR* 1.4 74.8 - - - +
146B GLY* 1.3 63.1 + - - +
225B ASP* 3.1 29.5 + - - +
226B SER* 3.1 17.0 + - - +
227B ALA* 2.8 39.7 + - + +
245B LEU* 3.6 14.2 - - - +
248B ARG* 3.4 9.4 - - - +
249B SER* 2.8 52.6 + - - +
251B PHE* 3.3 33.5 - - + -
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Residues in contact with GLY 146 (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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145B GLN* 1.3 83.5 - - - +
147B LEU* 1.3 60.9 + - - -
225B ASP* 3.5 5.0 - - - -
226B SER* 2.7 39.0 + - - -
245B LEU* 3.7 5.8 - - - +
247B PHE 3.1 13.2 - - - -
249B SER* 3.6 13.7 - - - -
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Residues in contact with LEU 147 (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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146B GLY* 1.3 74.1 - - - -
148B THR* 1.3 63.1 + - - +
181B SER* 6.0 0.2 - - - +
182B VAL* 3.6 39.5 - - + -
185B TYR* 3.8 18.2 - - + -
186B PHE* 4.7 0.2 - - + -
223B ILE* 4.9 0.7 - - + -
224B TRP 3.6 9.6 - - - +
225B ASP* 3.8 17.9 - - - +
245B LEU* 3.3 6.3 - - - -
246B PHE* 3.1 61.1 + - + -
247B PHE* 2.8 40.6 + - + +
249B SER* 4.8 4.3 - - - +
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Residues in contact with THR 148 (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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146B GLY 4.0 0.4 + - - -
147B LEU* 1.3 74.9 - - - +
149B ILE* 1.3 71.0 + - - +
223B ILE* 3.7 4.9 - - - +
224B TRP 3.1 27.3 + - - +
226B SER* 3.8 26.9 - - - -
229B LEU* 3.7 26.4 - - + +
230B GLU* 4.7 4.7 - - - +
241B THR* 3.9 17.5 + - + -
242B THR 3.4 9.0 + - - -
243B GLY 4.0 4.3 + - - -
244B GLU 3.1 20.9 + - - -
245B LEU* 4.5 2.0 - - - -
246B PHE* 4.2 3.8 - - - -
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Residues in contact with ILE 149 (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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148B THR* 1.3 83.3 + - - +
150B LEU* 1.3 61.0 + - - +
151B VAL* 4.2 4.9 - - + -
157B ILE* 4.8 4.0 - - + -
159B GLY* 3.6 37.9 - - - +
160B ILE* 3.6 13.9 - - + +
165B LEU* 4.0 13.5 - - + -
221B ALA* 3.9 27.4 - - + -
222B PHE 3.5 5.4 - - - +
223B ILE* 4.0 14.4 - - + -
229B LEU* 4.2 2.9 - - - -
241B THR* 3.1 4.5 - - - -
242B THR* 2.8 49.5 + - + +
246B PHE* 3.9 13.9 - - + -
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Residues in contact with LEU 150 (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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149B ILE* 1.3 72.8 - - - +
151B VAL* 1.3 63.6 + - - +
211B ILE* 4.2 17.5 - - + -
214B VAL* 4.2 12.6 - - + +
221B ALA* 3.4 6.6 - - - -
222B PHE* 2.8 42.2 + - + +
229B LEU* 3.8 49.8 - - + +
232B GLU* 4.8 2.2 - - + -
233B ALA* 4.5 3.6 - - + +
239B LEU* 4.0 38.6 - - + -
240B VAL 3.5 20.0 - - - +
241B THR* 4.0 4.0 - - + +
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Residues in contact with VAL 151 (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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149B ILE* 4.0 9.8 + - + -
150B LEU* 1.3 76.2 - - - +
152B LYS* 1.3 70.1 + - - +
155B THR* 3.7 31.6 - - + +
157B ILE* 4.6 11.0 - - + -
214B VAL* 3.7 8.5 - - - -
220B HIS 3.4 22.9 - - - +
221B ALA* 4.0 10.8 - - + -
239B LEU* 3.6 5.9 - - - +
240B VAL* 2.8 49.8 + - + +
242B THR* 4.7 14.1 - - + -
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Residues in contact with LYS 152 (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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151B VAL* 1.3 80.9 - - - +
153B LYS* 1.4 74.5 + - - +
154B GLY 3.2 0.2 + - - -
155B THR* 3.0 30.2 + - - +
214B VAL* 3.6 28.2 - - + +
215B ARG* 2.8 25.3 + - - +
217B ASN* 3.9 21.9 - - - +
220B HIS* 4.6 1.8 + - - +
238B ASP* 2.8 44.3 + - - +
239B LEU* 4.4 1.6 - - + -
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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