Contacts of the strand formed by residues 202 - 210 (chain D) in PDB entry 1LFD
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 202 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D MET* 1.3 73.4 - - - +
203D GLU* 1.3 59.1 + - - +
204D TYR* 3.7 23.8 - - + +
249D GLU* 3.1 27.2 + - - +
250D THR 3.8 4.1 + - - -
251D CYS* 3.4 5.2 - - - +
252D LEU* 2.8 31.9 + - - +
367D LYS* 3.8 21.5 - - - +
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Residues in contact with GLU 203 (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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201D MET 3.7 3.4 + - - +
202D THR* 1.3 79.9 - - - +
204D TYR* 1.3 69.2 + - - +
205D LYS* 3.7 20.3 + - + +
252D LEU* 3.4 27.8 - - + +
254D ASP* 3.1 40.4 - - - +
276D GLU* 3.3 12.2 - - - +
367D LYS* 5.2 1.7 + - - -
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Residues in contact with TYR 204 (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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202D THR* 3.7 25.0 - - + +
203D GLU* 1.3 78.1 - - - +
205D LYS* 1.3 62.1 + - - +
206D LEU* 3.3 19.6 - - + +
249D GLU* 2.9 20.6 + - - -
251D CYS* 3.6 35.7 - - + -
252D LEU 3.0 7.6 + - - +
253D LEU* 4.1 5.6 - - + -
254D ASP* 3.0 29.0 + - - +
276D GLU* 3.4 4.7 - - - -
360D VAL* 3.8 23.6 - - + -
363D ILE* 3.9 34.8 - - + -
364D ARG* 3.0 29.2 + - + +
367D LYS* 4.3 8.8 + - - -
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Residues in contact with LYS 205 (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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203D GLU* 3.7 23.1 + - + +
204D TYR* 1.3 71.8 - - - +
206D LEU* 1.3 62.4 + - - +
207D VAL* 4.7 2.0 - - + -
254D ASP* 3.7 14.5 + - + +
274D THR* 3.5 24.2 - - - +
275D GLY* 3.8 4.8 - - - -
276D GLU* 2.8 58.6 + - + +
277D GLY 3.1 8.0 + - - +
363D ILE* 5.2 0.4 - - - -
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Residues in contact with LEU 206 (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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204D TYR* 3.3 35.2 - - + +
205D LYS* 1.3 73.9 - - - +
207D VAL* 1.3 62.8 + - - +
208D VAL* 4.3 0.7 - - + -
253D LEU* 3.8 25.4 - - + -
254D ASP 2.8 17.6 + - - +
255D ILE* 3.4 11.7 - - + -
256D LEU* 3.0 24.4 + - - +
277D GLY 3.6 5.8 - - - +
356D PHE* 4.0 42.6 - - + +
359D LEU* 4.0 20.4 - - + -
360D VAL* 4.1 9.2 - - + -
363D ILE* 4.7 5.4 - - + -
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Residues in contact with VAL 207 (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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205D LYS* 4.4 2.0 - - + +
206D LEU* 1.3 79.2 - - - +
208D VAL* 1.3 59.9 + - - +
209D VAL* 3.8 10.2 + - + -
256D LEU* 3.7 17.5 - - + +
258D THR* 3.7 25.8 - - + -
271D TYR* 3.7 24.7 - - + +
275D GLY* 3.7 30.1 - - - -
277D GLY 2.9 6.6 + - - +
278D PHE* 3.3 15.7 - - + +
279D LEU* 2.8 31.8 + - - +
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Residues in contact with VAL 208 (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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206D LEU* 5.9 0.4 - - + -
207D VAL* 1.3 73.4 - - - +
209D VAL* 1.3 60.7 + - - +
216D LYS* 3.6 36.6 - - + +
219D LEU* 5.2 1.8 - - + -
220D THR* 3.7 19.7 - - - +
255D ILE* 3.9 19.3 - - + -
256D LEU 3.1 10.0 + - - +
257D ASP* 4.6 3.1 - - - -
258D THR* 2.9 26.2 + - - -
279D LEU* 3.7 12.6 - - + +
281D VAL* 3.8 20.9 - - + -
356D PHE* 3.9 16.8 - - + -
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Residues in contact with VAL 209 (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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207D VAL* 3.9 9.2 - - + -
208D VAL* 1.3 77.1 - - - +
210D GLY* 1.3 59.1 + - - +
216D LYS* 3.3 8.3 - - - -
258D THR* 3.8 4.0 - - - +
271D TYR* 3.5 37.2 - - + +
272D MET* 5.1 2.0 - - + -
278D PHE* 4.4 9.4 - - + -
279D LEU 2.9 17.4 + - - +
280D CYS* 3.9 23.1 - - - -
281D VAL* 2.9 30.8 + - - +
293D ILE* 5.0 0.2 - - + -
296D TYR* 3.8 22.2 - - + -
300D ILE* 4.4 8.7 - - + -
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Residues in contact with GLY 210 (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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209D VAL* 1.3 80.0 - - - +
211D ALA* 1.3 70.2 + - - +
214D VAL* 4.4 1.1 - - - -
216D LYS* 3.0 15.8 + - - +
258D THR* 4.8 0.4 + - - -
259D ALA 4.4 0.5 - - - +
260D GLY* 3.4 5.0 - - - -
281D VAL 3.4 14.8 - - - -
293D ILE* 4.3 4.7 - - - -
296D TYR* 3.2 27.0 + - - -
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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