Contacts of the strand formed by residues 297 - 306 (chain B) in PDB entry 1EBF
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 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B LYS* 4.0 1.6 - - - +
291B VAL* 3.3 1.4 - - - -
292B ASP* 2.6 45.5 + - - +
295B THR* 2.6 32.6 + - - -
296B LYS* 1.3 72.9 - - - +
298B VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL* 3.3 26.5 - - + -
228B GLY* 4.8 0.7 - - - -
233B VAL* 4.3 8.1 - - + -
235B VAL* 3.9 24.0 - - + -
241B PHE* 3.5 45.7 - - + +
242B PRO* 3.6 6.2 - - - +
290B LYS 3.1 3.8 - - - -
291B VAL* 3.3 33.7 - - + -
296B LYS 4.0 1.8 + - - +
297B SER* 1.3 77.8 - - - +
299B SER* 1.3 69.6 + - - +
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Residues in contact with SER 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL* 4.5 0.3 - - - +
241B PHE* 3.9 3.1 - - - -
242B PRO* 3.3 28.3 - - - -
288B ILE* 5.8 0.7 - - - +
289B GLY* 3.5 0.9 - - - -
290B LYS* 2.5 61.9 + - - +
298B VAL* 1.3 79.7 - - - +
300B VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B VAL* 3.3 32.1 - - + -
221B ALA* 4.0 2.9 - - - -
224B VAL* 4.0 12.8 - - + -
241B PHE* 3.6 24.0 - - + -
242B PRO* 3.1 4.4 + - - +
243B VAL* 3.7 23.0 - - + -
244B GLN* 3.1 17.0 + - - +
287B PHE* 3.6 15.7 - - + -
288B ILE* 3.0 14.6 - - - +
289B GLY* 4.1 1.8 - - - -
299B SER* 1.3 81.9 - - - +
301B GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLN* 3.5 17.7 - - - -
287B PHE* 3.8 14.1 - - - -
288B ILE* 2.8 37.8 + - - +
300B VAL* 1.3 77.6 - - - +
302B ILE* 1.3 64.7 + - - -
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Residues in contact with ILE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B PHE* 3.5 34.5 - - + -
244B GLN* 2.9 25.6 + - - +
246B LEU* 4.0 10.3 - - + -
271B LEU* 3.8 22.9 - - + -
274B LEU* 4.2 13.9 - - + -
285B LEU* 3.9 28.3 - - + -
286B ARG 3.2 14.1 - - - +
287B PHE* 3.9 10.1 - - + -
301B GLY* 1.3 73.6 - - - -
303B GLU* 1.3 66.0 + - - +
304B LYS* 5.7 0.9 - - + +
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLU* 4.1 5.7 - - - +
285B LEU* 3.8 1.9 - - - -
286B ARG 2.9 29.9 + - - +
288B ILE* 3.7 13.2 - - + +
290B LYS* 2.7 37.6 + - - -
302B ILE* 1.3 79.1 - - - +
304B LYS* 1.3 75.3 + - - +
305B TYR* 3.3 38.4 + - + +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B LEU* 3.8 22.5 - - + +
277B GLU* 4.1 16.0 + - - +
278B ALA* 4.1 19.3 - - + +
281B GLU* 4.3 16.6 - - - +
283B LYS* 3.4 32.5 + - + +
284B VAL 3.2 6.5 - - - +
285B LEU* 3.8 15.5 - - + +
302B ILE* 5.7 0.8 - - + +
303B GLU* 1.3 84.8 - - - +
305B TYR* 1.3 72.9 + - - +
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Residues in contact with TYR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLU* 3.0 32.4 + - - -
283B LYS* 3.6 6.3 - - - +
284B VAL* 2.7 47.8 + - + +
286B ARG* 3.9 15.3 - - + -
288B ILE* 3.7 22.2 - - + +
303B GLU* 3.3 48.6 + - + -
304B LYS* 1.3 79.1 - - - +
306B ASP* 1.3 64.4 + - - +
309B HIS* 3.6 39.0 - + + +
311B PHE* 3.5 26.9 - + + -
312B ALA* 5.0 0.7 - - + -
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Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B GLU 5.3 0.5 - - - +
282B ASN* 3.7 20.9 + - - +
283B LYS* 4.0 12.0 - - + +
305B TYR* 1.3 73.6 - - - +
307B TYR* 1.3 59.4 + - - +
308B SER* 2.7 40.8 + - - +
309B HIS* 2.6 38.3 + - + +
312B ALA* 3.7 4.2 - - - +
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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