Contacts of the strand formed by residues 188 - 196 (chain D) in PDB entry 3F12
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 TYR 188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D THR* 5.3 2.4 + - - -
122D THR* 4.7 13.5 - - - +
156D ASP* 3.0 21.1 + - - -
157D TYR* 2.9 43.1 + - + +
158D PHE* 3.7 28.4 - + - -
159D PRO* 4.4 7.0 - - + -
160D GLU* 3.6 40.5 - - + +
180D ALA* 4.4 3.6 - - + -
181D VAL 3.4 15.0 - - - -
182D LEU* 3.6 41.5 - - + +
187D LEU* 1.3 74.0 - - - +
189D SER* 1.3 67.5 + - - +
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Residues in contact with SER 189 (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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179C THR* 5.2 8.1 + - - +
153D LEU* 4.7 6.8 - - - +
154D VAL 3.2 12.8 + - - -
155D LYS* 3.9 21.9 - - - +
157D TYR* 3.6 3.3 - - - -
179D PRO 4.9 0.2 - - - +
180D ALA* 4.3 0.7 - - - -
181D VAL* 2.8 40.9 + - - +
183D GLN* 4.0 19.7 + - - -
188D TYR* 1.3 82.9 - - - +
190D LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 190 (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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153D LEU* 3.5 6.4 - - - +
154D VAL* 2.7 56.5 + - + +
157D TYR* 3.9 7.6 - - - +
160D GLU* 5.7 0.2 - - - +
162D VAL* 3.5 31.9 - - + +
164D VAL* 3.8 11.0 - - + -
177D THR* 4.4 11.2 - - + -
178D PHE* 3.8 18.4 - - - +
179D PRO 5.2 0.9 - - - -
180D ALA* 3.6 20.0 - - + +
189D SER* 1.3 75.9 - - - +
191D SER* 1.3 78.7 - - - +
192D SER* 3.7 3.4 - - - +
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Residues in contact with SER 191 (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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134C VAL* 4.9 6.5 - - - -
177C SER* 2.7 35.6 + - - -
179C THR* 5.5 2.1 + - - -
136D LEU* 5.3 2.2 - - - -
152D CYS 3.4 9.9 - - - -
153D LEU* 4.1 17.9 - - - -
178D PHE* 3.0 31.1 + - - +
190D LEU* 1.3 81.5 - - - +
192D SER* 1.3 61.1 + - - +
193D VAL* 5.0 4.5 - - - -
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Residues in contact with SER 192 (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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151D GLY* 3.1 1.4 - - - -
152D CYS* 2.9 35.4 + - - +
154D VAL* 5.8 0.2 - - - -
164D VAL* 3.2 33.8 - - - +
166D TRP* 3.2 20.8 + - - -
175D VAL* 4.5 0.9 - - - +
176D HIS 3.5 4.8 + - - -
177D THR* 2.6 28.3 + - - +
190D LEU* 3.7 2.4 - - - +
191D SER* 1.3 75.4 - - - +
193D VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 193 (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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119C PHE* 4.9 3.8 - - + -
134C VAL* 5.8 0.7 - - + -
136C LEU* 3.9 29.6 - - + -
138C ASN* 5.6 0.2 - - - +
177C SER* 4.7 5.2 - - - +
136D LEU* 4.3 13.7 - - + -
150D LEU 3.3 18.4 - - - +
151D GLY* 3.7 1.1 - - - -
166D TRP* 3.8 10.1 + - - -
174D GLY 5.0 0.2 - - - +
175D VAL* 3.8 1.7 - - - -
176D HIS* 3.0 48.7 + - + +
178D PHE* 4.0 17.3 - - + -
191D SER* 4.6 4.5 - - - +
192D SER* 1.3 81.9 + - - +
194D VAL* 1.3 69.7 + - - +
195D THR* 5.6 2.0 - - + -
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Residues in contact with VAL 194 (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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149D ALA* 3.1 3.8 - - - +
150D LEU* 2.8 44.4 + - + -
166D TRP* 4.6 13.5 - - + -
171D LEU* 4.2 17.9 - - + -
173D SER 3.8 7.2 - - - +
174D GLY 3.5 7.4 - - - -
175D VAL* 3.5 41.7 - - + +
193D VAL* 1.3 78.8 - - - +
195D THR* 1.3 64.5 + - - +
196D VAL* 3.4 26.4 + - + -
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Residues in contact with THR 195 (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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117C PHE* 5.7 4.9 - - + -
136C LEU* 5.4 2.7 - - + -
138C ASN* 2.9 29.6 - - - +
139C ASN* 5.4 0.2 - - - +
147D THR* 4.6 8.7 + - - +
148D ALA 3.1 11.2 - - - -
149D ALA* 4.1 7.9 - - + +
173D SER 4.5 4.3 - - - +
174D GLY* 3.5 29.1 + - - +
176D HIS* 5.5 0.4 - - + +
193D VAL* 5.6 1.1 - - + -
194D VAL* 1.3 77.1 - - - +
196D VAL* 1.3 62.5 + - - +
197D PRO* 4.4 1.6 - - - +
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Residues in contact with VAL 196 (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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147D THR* 2.9 14.8 + - - -
148D ALA* 2.6 34.3 + - + +
150D LEU* 3.2 38.4 - - + -
171D LEU* 4.7 5.6 - - + -
194D VAL* 3.4 16.3 + - + -
195D THR* 1.3 75.0 - - - +
197D PRO* 1.3 70.6 - - + +
198D SER 5.2 2.2 - - - +
206D TYR* 3.5 38.8 - - + +
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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