Contacts of the strand formed by residues 188 - 197 (chain D) in PDB entry 3LBF
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 188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C ARG* 5.7 2.4 + - - -
190C ILE* 3.4 25.7 - - + +
191C ILE 3.1 13.2 - - - +
192C ASP* 3.9 16.4 - - + +
184D ARG* 3.4 6.2 - - - +
185D ARG* 2.8 44.1 + - + +
186D GLY 3.3 0.2 - - - -
187D GLY* 1.3 79.1 - - - +
189D PHE* 1.3 67.1 + - - +
190D ILE* 4.1 15.2 - - - +
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Residues in contact with PHE 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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180C LYS* 5.7 7.0 - - - -
189C PHE 3.6 1.9 - - - +
190C ILE* 3.4 4.9 - - - +
191C ILE* 2.9 50.0 + - + +
193C THR* 5.9 2.7 - - - -
159D MET* 3.1 65.5 - - + -
160D THR* 4.4 2.2 - - - -
162D LEU* 4.2 3.1 - - + -
182D VAL* 3.8 19.1 - - + -
183D ARG 3.3 3.6 - - - -
184D ARG* 3.7 47.8 - - + -
187D GLY 4.4 9.4 - - - -
188D GLU* 1.3 82.2 - - - +
190D ILE* 1.3 61.0 + - - +
191D ILE* 4.0 1.1 - - + +
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Residues in contact with ILE 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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188C GLU* 3.5 37.0 - - - +
189C PHE 3.6 2.0 - - - -
190C ILE* 4.4 11.4 - - + +
181D ARG* 3.4 2.6 - - - +
182D VAL* 3.3 3.2 - - - -
183D ARG* 2.9 51.0 + - + +
185D ARG* 3.8 28.3 - - + -
188D GLU* 4.1 15.9 - - - +
189D PHE* 1.3 75.0 - - - +
191D ILE* 1.3 63.2 + - - +
192D ASP* 3.9 10.0 + - - +
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Residues in contact with ILE 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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159C MET* 4.4 12.6 - - + -
187C GLY 4.3 1.0 - - - +
188C GLU* 3.1 22.0 - - - +
189C PHE* 2.8 38.5 + - + +
191C ILE* 3.8 30.7 - - + -
154D ILE* 3.6 25.1 - - + -
159D MET* 5.2 0.4 - - - -
180D LYS* 4.3 24.0 - - + +
181D ARG 3.5 5.4 - - - +
182D VAL* 3.9 25.6 - - + -
189D PHE 4.7 1.3 - - - +
190D ILE* 1.3 75.8 - - - +
192D ASP* 1.3 70.4 + - - +
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Residues in contact with ASP 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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187C GLY 4.8 3.2 - - - -
188C GLU* 2.8 37.1 + - - +
180D LYS* 3.3 8.8 - - - +
181D ARG* 2.9 50.6 + - + +
190D ILE* 4.1 10.6 - - - +
191D ILE* 1.3 74.6 - - - +
193D THR* 1.3 66.2 + - - +
194D VAL* 5.8 0.4 - - + -
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Residues in contact with THR 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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187C GLY 4.6 13.1 + - - -
189C PHE* 5.8 0.3 - - - -
178D TYR* 4.0 34.3 - - + -
179D LEU 3.7 3.4 - - - +
180D LYS* 2.9 29.5 + - - +
192D ASP* 1.3 75.3 - - - +
194D VAL* 1.3 64.8 + - - +
195D GLU* 4.0 8.5 - - - +
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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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66D ARG* 5.1 12.6 - - - +
70D LEU* 4.2 20.9 - - + -
179D LEU* 2.8 48.9 + - + +
180D LYS 4.1 1.1 - - - -
181D ARG* 4.1 24.5 - - + +
192D ASP* 5.0 0.7 - - + -
193D THR* 1.3 77.4 - - - +
195D GLU* 1.3 77.3 + - + +
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Residues in contact with GLU 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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62D TYR* 3.8 20.8 + - - -
63D MET* 3.7 27.5 - - - +
66D ARG* 4.7 5.4 + - - +
178D TYR* 3.3 10.8 - - - +
179D LEU* 2.7 34.9 + - + -
193D THR* 3.8 4.1 - - - +
194D VAL* 1.3 97.5 - - + +
196D ALA* 1.3 75.9 + - - +
197D VAL* 4.1 6.3 - - + -
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Residues in contact with ALA 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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177D GLN 3.7 7.6 - - - +
178D TYR* 4.0 19.2 - - + -
195D GLU* 1.3 83.8 + - - +
197D VAL* 1.3 70.4 + - - +
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Residues in contact with VAL 197 (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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63D MET* 4.1 16.4 - - + -
171D PRO* 3.7 26.0 - - + -
177D GLN* 3.2 31.1 + - + +
178D TYR 3.9 4.0 - - - -
179D LEU* 3.7 29.6 - - + +
195D GLU* 4.0 18.8 - - + +
196D ALA* 1.3 81.4 - - - +
198D ARG* 1.3 64.3 + - - +
199D PHE* 3.8 14.6 - - + -
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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