Contacts of the strand formed by residues 270 - 282 (chain L) in PDB entry 6AHU
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 SER 270 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218L GLN* 2.8 40.6 + - - +
219L CYS 3.3 13.2 - - - -
220L PRO* 3.8 1.6 - - - -
221L VAL* 3.8 4.5 - - - +
266L CYS* 3.9 5.4 - - - -
267L PRO 3.9 13.7 - - - -
268L GLU* 4.1 4.0 - - - +
269L PRO* 1.3 76.0 - - - +
271L THR* 1.3 68.9 + - - +
272L VAL* 6.0 0.2 - - - +
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Residues in contact with THR 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218L GLN* 4.6 2.7 - - - -
219L CYS* 2.6 35.8 + - - +
220L PRO 4.9 2.4 + - - -
221L VAL* 3.4 16.9 - - - +
270L SER* 1.3 78.1 + - - +
272L VAL* 1.3 74.4 + - - +
273L VAL* 3.2 12.2 + - + +
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Residues in contact with VAL 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L GLU* 5.4 0.9 - - - +
216L ASP* 5.2 11.9 - - + +
217L LEU 4.1 4.3 - - - +
218L GLN* 4.7 15.5 - - + +
270L SER* 6.0 0.2 - - - +
271L THR* 1.3 77.5 - - - +
273L VAL* 1.3 68.3 + - - +
274L ALA* 4.2 1.5 + - - -
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Residues in contact with VAL 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L PRO* 3.9 15.0 - - + -
48L GLU* 3.7 23.3 - - + +
216L ASP* 3.4 3.5 - - - -
217L LEU* 2.8 44.3 + - + +
219L CYS* 3.7 25.4 - - + -
271L THR* 3.5 22.0 - - + +
272L VAL* 1.3 76.3 - - - +
274L ALA* 1.3 62.3 + - - +
275L LYS 3.3 23.7 + - - +
276L ALA* 5.6 0.4 - - + -
308L PRO* 6.3 3.8 - - + -
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Residues in contact with ALA 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L GLU* 4.4 11.3 + - + +
215L ARG* 3.4 8.3 + - - +
216L ASP* 2.8 34.2 + - - +
272L VAL* 4.2 2.9 + - - +
273L VAL* 1.3 75.0 - - - +
275L LYS* 1.3 70.0 + - + +
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Residues in contact with LYS 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L PRO 3.5 0.3 - - - -
48L GLU* 2.6 44.2 + - - +
49L CYS 4.1 9.4 - - - +
50L GLY* 3.7 32.2 - - - +
213L THR* 5.3 8.1 - - + -
214L LEU 3.5 4.3 - - - +
215L ARG* 4.7 11.2 - - + +
216L ASP 5.6 0.2 - - - -
217L LEU* 5.7 0.2 - - - -
273L VAL* 3.3 15.2 - - - +
274L ALA* 1.3 88.4 - - + +
276L ALA* 1.3 59.0 + - - +
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Residues in contact with ALA 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L LEU* 4.7 12.3 - - + -
46L ILE 3.9 5.4 - - - -
47L PRO* 4.2 2.5 - - + -
48L GLU 4.3 0.2 - - - +
49L CYS 5.0 1.6 - - - -
213L THR* 3.5 5.2 - - - +
214L LEU* 2.6 52.7 + - + +
217L LEU* 3.8 35.0 - - + -
275L LYS* 1.3 78.7 - - - +
277L TYR* 1.3 59.5 + - - +
278L LEU* 5.1 0.4 - - + -
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Residues in contact with TYR 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L PHE* 4.4 14.8 - + - -
45L LEU* 3.5 31.4 - - - +
46L ILE* 3.0 26.0 + - + +
49L CYS* 3.7 30.2 + - + +
50L GLY 5.8 2.7 - - - -
52L LEU* 3.3 45.7 - - + +
57L LYS* 4.2 2.3 + - - -
211L LEU* 3.3 29.6 - - + +
212L SER 3.7 14.8 - - - -
213L THR* 3.9 13.5 - - - +
276L ALA* 1.3 72.1 - - - +
278L LEU* 1.3 74.8 + - - +
279L CYS* 4.3 10.1 - - + -
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Residues in contact with LEU 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L PHE 4.5 0.7 - - - -
45L LEU* 3.8 16.4 - - + -
210L ALA 4.5 0.2 - - - -
211L LEU* 3.9 1.9 - - - -
212L SER* 2.8 56.7 + - - +
213L THR 5.0 0.2 - - - -
214L LEU* 3.9 30.7 - - + +
247L VAL* 4.2 19.3 - - + +
248L PHE* 3.7 37.2 - - + +
250L ASN* 4.8 11.0 - - - +
276L ALA* 4.5 0.9 - - + +
277L TYR* 1.3 84.0 - - - +
279L CYS* 1.3 63.3 + - - +
280L THR* 6.0 0.4 - - - +
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Residues in contact with CYS 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L SER* 3.3 22.7 + - - -
44L PHE* 3.6 53.5 + - + +
60L VAL* 4.1 6.5 - - - -
209L VAL* 4.9 0.7 - - - -
210L ALA 3.4 6.3 - - - -
211L LEU* 3.7 22.7 - - + -
248L PHE* 5.1 4.4 - - - -
277L TYR* 4.3 2.7 - - + -
278L LEU* 1.3 77.2 - - - +
280L THR* 1.3 78.4 + - - +
281L ILE* 3.9 16.8 - - - -
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Residues in contact with THR 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L ARG* 4.8 15.3 + - + +
42L VAL 3.9 0.2 - - - -
43L SER* 3.8 15.6 + - - +
208L LYS 3.2 6.1 - - - +
209L VAL* 3.5 1.2 - - - -
210L ALA* 3.0 45.5 + - + +
248L PHE* 6.0 2.4 - - - +
278L LEU* 6.0 0.5 - - - +
279L CYS* 1.3 79.6 + - - +
281L ILE* 1.3 62.7 + - - +
282L THR* 3.4 21.0 + - - +
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Residues in contact with ILE 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L TYR 3.4 6.9 - - - +
41L ARG* 3.9 0.9 - - - -
42L VAL* 2.9 52.3 + - + +
44L PHE* 3.9 20.2 - - + -
60L VAL* 3.8 35.2 - - + +
63L THR* 3.8 24.9 - - + +
207L PRO* 4.2 7.6 - - + -
208L LYS 3.4 3.6 - - - +
209L VAL* 5.0 3.4 - - + -
279L CYS* 3.9 5.2 - - - -
280L THR* 1.3 74.9 - - - +
282L THR* 1.3 60.0 + - - +
283L GLY 3.8 0.5 + - - -
285L ILE* 3.7 26.1 - - + +
293L LEU* 5.0 4.7 - - + -
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Residues in contact with THR 282 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L TYR* 3.3 38.4 - - + +
41L ARG* 5.2 3.9 - - + +
66L TYR* 4.8 1.7 + - - -
207L PRO* 3.3 2.3 - - - +
208L LYS* 2.5 64.7 + - + +
280L THR* 3.4 23.4 - - - +
281L ILE* 1.3 69.3 - - - +
283L GLY* 1.3 58.5 + - - +
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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