Contacts of the strand formed by residues 310 - 316 (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 PRO 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276D GLU 3.3 26.5 - - - +
277D GLY* 3.6 3.7 - - - -
278D PHE* 3.0 27.3 + - - -
309D VAL* 1.3 84.8 - - + +
311D MET* 1.3 61.6 + - - +
359D LEU* 4.0 2.9 - - + -
362D GLU* 4.1 8.1 - - + +
363D ILE* 3.6 34.1 - - + +
366D HIS* 3.7 43.0 - - + +
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Residues in contact with MET 311 (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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278D PHE* 3.2 10.1 - - + +
280D CYS* 3.5 27.6 - - + -
297D ARG* 3.6 35.9 - - + +
300D ILE* 3.8 29.6 - - + -
301D LYS* 6.0 0.4 - - + -
309D VAL* 3.3 31.2 + - + +
310D PRO* 1.3 78.1 - - - +
312D VAL* 1.3 73.8 + - - +
337D TYR* 6.0 0.2 - - - -
339D ILE* 3.4 41.5 - - + +
340D PRO* 3.5 4.9 - - - +
359D LEU* 3.8 3.9 - - - +
362D GLU* 4.3 7.0 + - - +
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Residues in contact with VAL 312 (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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278D PHE 3.1 5.9 + - - -
279D LEU* 3.8 12.4 - - + -
280D CYS* 3.0 26.2 + - - -
311D MET* 1.3 81.8 - - - +
313D LEU* 1.3 72.7 + - - +
314D VAL* 3.5 10.6 + - + +
339D ILE* 4.2 2.7 - - - -
340D PRO* 3.5 24.9 - - + +
342D ILE* 4.0 24.9 - - + -
355D ALA 4.3 3.1 - - - +
358D THR* 4.3 6.5 - - + -
359D LEU* 3.7 34.3 - - + +
362D GLU* 4.3 2.2 - - + -
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Residues in contact with LEU 313 (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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280D CYS* 3.5 16.8 - - + +
282D PHE* 3.8 24.2 - - + -
293D ILE* 3.9 23.3 - - + -
312D VAL* 1.3 72.1 - - - +
314D VAL* 1.3 60.5 + - - +
330D ALA* 3.3 29.6 - - + +
333D LEU* 4.2 14.6 - - + -
334D ALA* 3.9 14.8 - - + +
337D TYR* 5.5 3.6 - - + -
339D ILE* 3.7 16.4 - - + +
340D PRO 3.0 13.2 + - - +
341D TYR* 3.4 17.2 - - + -
342D ILE 2.9 26.3 + - - -
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Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D LEU* 4.1 15.9 - - + -
279D LEU* 3.7 35.0 - - + -
280D CYS 2.8 13.6 + - - +
281D VAL* 4.2 7.9 - - + -
282D PHE* 3.0 35.9 + - - +
312D VAL* 3.9 7.2 - - + +
313D LEU* 1.3 78.0 - - - +
315D GLY* 1.3 59.8 + - - +
316D ASN 4.0 3.4 - - - +
342D ILE 3.2 7.6 - - - +
344D THR* 3.3 31.9 - - + +
355D ALA* 4.0 14.4 - - + -
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Residues in contact with GLY 315 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282D PHE* 3.7 25.1 - - - -
284D ILE* 4.1 8.3 - - - +
314D VAL* 1.3 69.2 - - - +
316D ASN* 1.3 64.7 + - - +
318D CYS* 4.3 1.4 - - - +
341D TYR* 3.9 14.0 - - - -
342D ILE 2.9 11.3 + - - -
343D GLU* 3.2 8.7 - - - +
344D THR* 2.8 22.6 + - - +
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Residues in contact with ASN 316 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214D VAL 2.9 28.8 + - - +
215D GLY* 3.5 10.1 + - - -
219D LEU* 3.1 17.0 - - + +
281D VAL* 3.9 11.4 - - + -
282D PHE 2.9 12.0 + - - +
283D ALA* 3.6 0.9 - - - -
284D ILE* 3.2 21.5 + - - +
314D VAL 3.5 1.4 + - - -
315D GLY* 1.3 74.7 - - - +
317D LYS* 1.3 80.8 + - - +
344D THR* 2.9 24.2 + - - +
345D SER 3.5 0.7 + - - -
346D ALA 3.4 4.2 + - - -
2380D GNP 3.1 33.7 + - - +
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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