Contacts of the strand formed by residues 277 - 283 (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 GLY 277 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D LYS 3.1 6.7 + - - +
206D LEU* 3.6 1.0 - - - -
207D VAL* 2.9 26.9 + - - +
276D GLU* 1.3 78.8 - - - +
278D PHE* 1.3 67.0 + - - -
310D PRO* 3.6 16.6 - - - -
359D LEU* 3.9 13.9 - - - -
363D ILE* 3.9 8.8 - - - +
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Residues in contact with PHE 278 (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* 3.3 33.0 - - + +
209D VAL* 4.4 7.4 - - + -
271D TYR 4.1 2.0 - - - -
272D MET* 3.0 48.9 - - + -
275D GLY* 3.4 24.5 - - - -
276D GLU 4.4 0.4 - - - -
277D GLY* 1.3 73.7 - - - -
279D LEU* 1.3 61.1 + - - +
280D CYS* 3.5 4.1 + - - -
300D ILE* 3.7 44.0 - - + -
304D LYS* 4.1 0.9 - - - -
309D VAL* 3.8 13.2 - - + -
310D PRO 3.0 19.0 + - - +
311D MET* 3.2 9.5 - - + +
312D VAL 3.1 24.3 + - - -
359D LEU* 3.6 7.0 - - - +
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Residues in contact with LEU 279 (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 2.8 14.2 + - - +
208D VAL* 4.1 15.3 - - + -
209D VAL* 2.9 29.6 + - - +
219D LEU* 5.1 4.3 - - + -
278D PHE* 1.3 72.0 - - - +
280D CYS* 1.3 61.2 + - - +
281D VAL* 3.3 7.2 + - + +
312D VAL* 3.8 10.8 - - + -
314D VAL* 3.7 26.7 - - + -
355D ALA* 3.4 27.8 - - + +
356D PHE* 3.5 45.3 - - + +
359D LEU* 3.7 19.9 - - + +
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Residues in contact with CYS 280 (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* 3.7 21.8 - - - -
278D PHE* 4.4 1.3 - - - -
279D LEU* 1.3 69.8 - - - +
281D VAL* 1.3 57.2 + - - +
293D ILE* 3.5 24.2 - - + +
297D ARG* 5.0 7.4 - - - -
300D ILE* 4.0 12.3 - - - -
311D MET* 3.5 36.8 - - + -
312D VAL 3.0 12.7 + - - +
313D LEU* 3.5 12.3 - - + +
314D VAL 2.8 29.7 + - - -
339D ILE* 5.8 0.7 - - + -
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Residues in contact with VAL 281 (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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208D VAL* 3.8 19.5 - - + -
209D VAL 2.9 14.6 + - - +
210D GLY* 3.4 13.3 - - - -
211D ALA 4.2 1.6 + - - -
214D VAL* 3.9 24.1 - - + +
216D LYS* 4.3 2.7 - - + +
219D LEU* 3.8 28.5 - - + -
279D LEU* 3.6 18.8 - - + +
280D CYS* 1.3 74.3 - - - +
282D PHE* 1.3 73.0 + - - +
289D SER 4.8 0.7 - - - +
293D ILE* 3.4 15.4 - - - +
314D VAL* 3.5 14.1 - - + +
316D ASN* 3.9 11.2 - - + -
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Residues in contact with PHE 282 (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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214D VAL* 4.0 11.0 - - - -
281D VAL* 1.3 75.1 - - - +
283D ALA* 1.3 77.1 + - - +
284D ILE* 4.1 8.3 - - + -
289D SER* 3.6 26.5 - - - +
290D PHE* 3.7 32.1 - + + -
293D ILE* 4.5 4.0 - - + -
313D LEU* 3.8 24.2 - - + -
314D VAL 3.0 26.4 + - - +
315D GLY* 3.8 7.2 - - - -
316D ASN* 2.9 27.4 + - - +
325D VAL* 3.8 15.7 - - + -
330D ALA* 3.6 23.1 - - + -
341D TYR* 3.8 22.4 - + - -
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Residues in contact with ALA 283 (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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213D GLY 5.3 0.2 - - - +
214D VAL* 3.9 13.5 - - - +
282D PHE* 1.3 82.0 - - - +
284D ILE* 1.3 57.6 + - - +
285D ASN* 3.1 20.0 - - - +
286D ASN* 3.1 40.5 + - + +
289D SER* 3.0 7.0 + - - +
316D ASN 3.6 4.9 - - - -
317D LYS* 3.8 23.3 - - + +
325D VAL* 4.0 0.7 - - - +
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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