Contacts of the strand formed by residues 270 - 278 (chain X) in PDB entry 2AE0
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 270 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39X PHE* 4.1 26.1 - - + -
57X GLN* 5.6 1.0 - - - +
60X VAL* 3.6 18.3 - - - +
61X TYR* 3.2 32.1 - - - -
64X VAL* 4.3 11.2 - - + -
268X GLY 3.5 0.6 + - - -
269X THR* 1.3 74.5 - - - +
271X LEU* 1.3 65.3 + - - +
292X LEU* 4.3 11.2 - - + -
293X MET 3.7 3.1 - - - +
294X VAL* 4.7 1.5 - - - +
332X VAL* 3.6 4.7 - - - -
333X LEU* 3.0 43.1 + - + +
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Residues in contact with LEU 271 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258X VAL* 3.8 19.5 - - + -
265X ILE* 4.2 6.3 - - + -
269X THR* 4.1 14.4 - - + +
270X THR* 1.3 81.9 - - - +
272X LEU* 1.3 60.0 + - - +
273X ALA 3.9 0.4 - - - -
291X ARG 3.8 0.3 - - - +
292X LEU* 3.3 9.9 - - - +
293X MET* 2.8 59.6 + - + +
295X ALA 4.8 3.6 - - - +
307X PHE* 3.7 37.5 - - + -
330X VAL* 4.0 17.9 - - + -
331X TRP 3.6 2.0 - - - -
332X VAL* 3.8 24.9 - - + -
333X LEU* 4.8 0.2 - - - -
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Residues in contact with LEU 272 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X PRO* 4.2 12.1 - - + -
29X ALA* 5.3 0.2 - - + -
33X PRO* 3.9 26.5 - - + -
67X TRP* 4.5 2.9 - - + -
74X THR* 4.1 21.1 - - + -
77X MET* 4.1 20.9 - - + -
271X LEU* 1.3 72.7 - - - +
273X ALA* 1.3 60.2 + - - +
290X LEU* 3.7 25.8 - - + -
291X ARG 3.6 7.6 - - - +
292X LEU* 4.1 8.5 - - + -
330X VAL* 3.4 1.7 - - - +
331X TRP* 2.9 53.4 + - + +
333X LEU* 4.1 16.7 - - + +
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Residues in contact with ALA 273 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X PHE* 4.1 7.4 - - + -
271X LEU 3.9 0.2 - - - -
272X LEU* 1.3 77.1 - - - +
274X GLU* 1.3 60.0 + - - +
275X VAL* 3.5 6.2 + - + +
289X GLU 3.1 4.2 - - - +
290X LEU* 3.3 7.7 - - - -
291X ARG 2.8 39.6 + - - +
293X MET* 3.7 29.4 - - + -
329X ARG 3.4 10.1 - - - +
330X VAL* 3.8 13.9 - - + -
331X TRP* 4.8 0.4 - - - -
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Residues in contact with GLU 274 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X ALA* 3.3 25.3 - - + +
30X VAL* 4.3 5.5 + - - +
98X PHE* 4.2 1.4 - - - -
273X ALA* 1.3 70.9 - - - +
275X VAL* 1.3 62.0 + - - +
288X TYR* 3.6 20.8 - - + +
289X GLU 3.5 0.6 - - - -
290X LEU* 3.8 28.3 + - + +
328X GLY* 3.2 25.8 - - - -
329X ARG* 2.8 46.3 + - - +
331X TRP* 3.9 21.5 - - + -
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Residues in contact with VAL 275 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X PHE* 4.6 3.6 - - + -
273X ALA* 4.1 20.2 - - + +
274X GLU* 1.3 73.2 - - - +
276X PRO* 1.3 82.4 - - + +
277X LEU* 3.5 7.1 + - + +
288X TYR* 3.1 4.3 - - - -
289X GLU* 2.8 46.2 + - + +
291X ARG* 4.9 13.2 - - + +
293X MET* 4.6 10.3 - - - -
309X ILE* 3.6 34.1 - - + -
311X GLN* 5.4 6.1 - - - +
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Residues in contact with PRO 276 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X ARG 4.7 0.4 - - - +
98X PHE* 3.9 13.0 - - + -
274X GLU 3.7 7.4 - - - +
275X VAL* 1.3 99.6 - - + +
277X LEU* 1.3 61.0 + - - +
278X LEU* 4.2 8.5 + - + +
284X PHE* 3.9 17.7 - - + -
287X GLN 3.7 1.1 - - - +
288X TYR* 3.6 12.1 - - + -
326X HIS* 3.9 24.5 - - + -
327X TYR* 3.4 31.6 - - - +
328X GLY* 3.9 4.7 - - - -
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Residues in contact with LEU 277 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275X VAL* 4.1 12.3 - - + +
276X PRO* 1.3 76.5 - - - +
278X LEU* 1.3 63.2 + - - +
284X PHE* 3.4 8.8 - - - -
285X ASN* 3.0 43.3 + - - +
287X GLN* 2.9 40.9 + - + +
288X TYR 4.7 1.1 - - - +
289X GLU* 3.5 46.7 - - + +
320X ARG* 6.6 0.2 - - - -
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Residues in contact with LEU 278 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276X PRO* 4.2 11.0 - - + +
277X LEU* 1.3 84.6 - - - +
279X ASP* 1.3 69.3 + - - +
282X GLY* 4.0 9.6 - - - +
283X LYS 3.2 5.2 - - - +
284X PHE* 4.1 5.4 - - + +
285X ASN* 4.0 9.2 + - - -
319X HIS 4.9 4.5 - - - +
320X ARG* 3.8 20.0 - - - +
321X ALA 4.5 1.6 - - - +
322X GLY* 3.7 30.3 - - - +
326X HIS* 3.5 49.1 - - + +
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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