Contacts of the strand formed by residues 195 - 207 (chain H) in PDB entry 1CBV
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 THR 195 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167H LEU* 3.6 25.7 - - + +
191H VAL* 3.7 0.8 - - - +
192H PRO* 2.5 34.2 + - + +
193H SER 3.2 0.4 + - - -
194H SER* 1.3 89.2 - - - +
196H TRP* 1.3 61.5 + - - +
198H SER* 3.3 4.8 + - - -
199H GLN* 2.5 69.0 + - - +
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Residues in contact with TRP 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H ALA* 4.3 4.7 - - + -
134H PRO* 4.0 33.0 - - + -
138H ASP* 4.9 11.2 - - - -
139H THR* 4.1 22.7 - - + +
144H VAL* 4.8 4.7 - - + -
146H LEU* 3.6 39.7 - - + +
191H VAL* 3.9 23.6 - - + -
192H PRO 3.3 5.9 + - - +
193H SER* 3.3 16.6 + - - +
194H SER 5.2 0.2 - - - -
195H THR* 1.3 79.8 - - - +
197H PRO* 1.3 83.0 - - + +
198H SER* 3.5 2.8 + - - -
199H GLN 3.9 15.1 + - - -
201H VAL* 4.2 5.4 - - + +
218H LEU 3.8 26.1 + - - -
219H GLU* 3.8 28.0 - - - -
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Residues in contact with PRO 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H ASP* 4.3 14.6 - - - +
196H TRP* 1.3 112.0 - - + +
198H SER* 1.3 64.5 + - - +
199H GLN 3.3 7.2 + - - +
200H THR* 5.3 0.7 - - - -
219H GLU* 3.3 36.0 - - - +
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Residues in contact with SER 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195H THR* 3.3 6.8 + - - -
196H TRP 4.9 1.0 - - - -
197H PRO* 1.3 80.1 - - - +
199H GLN* 1.3 79.6 + - - +
200H THR* 3.6 8.8 + - - +
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Residues in contact with GLN 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H GLY* 5.6 2.7 - - - +
167H LEU* 3.6 28.3 - - + +
194H SER 5.0 0.2 + - - -
195H THR* 2.5 62.1 + - + +
196H TRP* 3.9 17.3 + - - -
197H PRO 3.9 6.2 - - - +
198H SER* 1.3 91.7 - - - +
200H THR* 1.3 59.5 + - - +
201H VAL* 3.3 9.0 + - - +
218H LEU 5.5 0.2 - - - +
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Residues in contact with THR 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H ASN* 2.6 31.0 + - - +
164H SER* 4.7 2.6 - - - -
165H GLY 4.9 1.9 + - - -
197H PRO 5.3 1.6 - - - -
198H SER 3.8 8.0 + - - -
199H GLN* 1.3 68.0 - - - +
201H VAL* 1.3 59.1 + - - +
202H THR* 5.0 2.5 - - - +
217H LYS* 3.7 42.8 - - + +
218H LEU 5.6 1.1 - - - +
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Residues in contact with VAL 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H LEU* 3.5 31.6 - - + -
162H TRP* 3.4 33.2 - - + -
163H ASN 3.0 9.0 - - - +
164H SER* 4.2 17.5 - - - -
167H LEU* 4.9 2.7 - - + -
189H VAL* 4.0 5.8 - - + -
191H VAL* 4.7 11.4 - - + -
196H TRP* 4.2 6.9 - - + +
199H GLN 3.3 11.4 + - - +
200H THR* 1.3 74.4 - - - +
202H THR* 1.3 71.4 + - - +
217H LYS* 3.5 5.5 - - - +
218H LEU* 3.1 31.9 + - + -
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Residues in contact with THR 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H TRP* 3.1 12.7 - - - -
163H ASN* 2.6 63.2 + - + -
200H THR* 4.5 2.9 - - - +
201H VAL* 1.3 77.7 + - - +
203H CYS* 1.3 75.3 - - - +
204H SER* 4.2 7.0 - - - +
215H ASP* 4.0 13.0 - - + +
216H LYS 3.4 22.2 - - - +
217H LYS* 4.1 7.3 - - - +
218H LEU 4.6 0.2 - - - +
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Residues in contact with CYS 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H VAL* 5.3 0.2 - - - -
148H CYS* 2.0 51.6 - - + -
160H VAL* 4.4 4.3 - - + -
161H THR 3.2 6.1 - - - +
162H TRP* 3.7 24.9 - - + -
202H THR* 1.3 74.2 - - - +
204H SER* 1.3 62.4 + - - +
205H VAL* 4.1 14.8 - - - -
214H VAL 3.8 1.7 - - - +
215H ASP* 3.5 5.7 - - - -
216H LYS* 3.3 31.6 + - - -
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Residues in contact with SER 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H THR 2.8 23.2 - - - +
160H VAL* 4.6 0.2 - - - +
161H THR* 2.6 46.6 + - - +
163H ASN* 5.4 4.0 + - - +
202H THR* 4.2 8.3 - - - +
203H CYS* 1.3 75.6 + - - +
205H VAL* 1.3 54.1 + - - +
206H ALA* 3.7 2.1 + - - +
213H THR* 5.7 5.8 - - - -
214H VAL 3.8 4.5 - - - -
215H ASP* 3.6 17.3 + - - -
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Residues in contact with VAL 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H PRO* 4.0 17.2 - - + +
129H VAL* 3.3 41.1 - - + -
150H VAL* 3.9 13.5 - - + -
158H VAL* 3.5 24.9 - - + -
159H THR 3.6 5.4 - - - -
160H VAL* 4.1 12.1 - - + -
203H CYS* 4.1 12.8 - - - -
204H SER* 1.3 72.7 - - - +
206H ALA* 1.3 58.4 + - - +
212H THR 3.8 1.4 - - - +
213H THR* 3.6 3.5 - - - -
214H VAL* 3.2 32.8 + - + +
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Residues in contact with ALA 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H VAL* 3.3 27.2 - - - +
159H THR* 3.4 19.1 + - + +
204H SER 3.7 1.9 + - - +
205H VAL* 1.3 75.1 - - - +
207H HIS* 1.3 64.8 + - - +
208H PRO* 3.8 6.0 - - + +
212H THR 3.1 6.1 - - - +
213H THR* 3.6 17.3 - - + +
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Residues in contact with HIS 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H THR* 4.6 0.4 - - + -
125H THR 3.0 25.3 + - - -
127H PRO* 4.1 22.8 - - + +
153H TYR* 3.5 34.5 - + + +
154H PHE 3.3 19.9 + - - -
155H PRO* 3.7 6.0 + - + +
157H SER 3.8 8.3 - - - -
158H VAL* 3.6 10.3 - - + -
206H ALA* 1.3 76.0 - - - +
208H PRO* 1.3 75.2 - - - +
209H ALA* 2.6 27.6 + - + -
210H SER* 3.1 8.8 + - - -
211H SER* 3.2 16.1 + - - -
212H THR* 2.9 17.5 + - - +
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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