Contacts of the strand formed by residues 278 - 285 (chain I) in PDB entry 5BRR
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 PHE 278 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235I MET* 4.9 6.3 - - - -
237I ILE* 6.2 0.9 - - + -
275I LEU* 5.7 3.4 - - + -
276I PRO* 3.5 21.1 + - + -
277I LYS* 1.3 76.2 - - - +
279I SER* 1.3 65.9 + - - +
280I LEU* 4.0 22.0 - - + -
326I ILE* 4.9 9.0 - - + -
327I GLU* 3.8 1.2 - - - +
328I VAL* 2.9 69.1 + - + +
358I PHE* 3.9 26.0 - + - -
360I PHE* 4.6 22.0 - + - -
376I VAL* 4.0 22.2 - - + -
379I PRO* 4.4 20.4 - - + -
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Residues in contact with SER 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278I PHE* 1.3 78.7 - - - +
280I LEU* 1.3 69.6 + - - +
281I GLU 4.4 0.3 + - - -
325I LYS* 4.5 7.2 - - - -
326I ILE 3.7 3.4 - - - -
327I GLU* 2.8 36.4 + - - +
379I PRO 5.2 3.7 + - - +
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Residues in contact with LEU 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I ASN* 3.3 43.7 - - + +
32I VAL 4.4 2.9 - - - +
33I VAL* 3.4 34.9 - - + +
278I PHE* 4.0 17.2 - - + -
279I SER* 1.3 87.8 - - - +
281I GLU* 1.3 61.3 + - - +
324I VAL 3.9 0.3 - - - +
325I LYS* 3.1 7.9 - - - +
326I ILE* 2.9 40.2 + - + +
360I PHE* 5.1 0.2 - - + -
375I GLN 4.4 0.7 - - - +
376I VAL* 4.2 24.2 - - + -
379I PRO* 4.5 8.7 - - + +
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Residues in contact with GLU 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I MET 4.4 2.3 - - - +
148I ILE* 4.0 17.0 - - - +
150I HIS* 4.6 8.4 - - - -
279I SER 4.4 0.2 + - - -
280I LEU* 1.3 77.2 - - - +
282I THR* 1.3 62.2 + - - +
283I GLU 4.4 0.5 + - - -
323I LYS* 3.4 38.3 + - - -
324I VAL 3.2 13.5 - - - +
325I LYS* 3.7 30.3 + - + +
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Residues in contact with THR 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I VAL* 5.7 1.3 - - + -
31I ASN 3.5 15.6 + - - -
32I VAL* 4.6 8.1 - - + -
33I VAL* 3.4 39.2 + - - +
281I GLU* 1.3 74.5 + - - +
283I GLU* 1.3 65.4 + - - +
284I VAL* 3.6 26.0 - - + +
322I GLN 3.8 1.2 - - - +
323I LYS* 3.3 4.4 - - - +
324I VAL* 2.8 34.0 + - - +
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Residues in contact with GLU 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I LEU* 3.4 24.5 - - + +
152I LEU* 3.2 26.1 + - + +
153I GLY* 2.6 36.2 + - - -
281I GLU 4.3 0.2 - - - -
282I THR* 1.3 79.7 - - - +
284I VAL* 1.3 67.9 + - - +
285I ASP 4.3 0.2 + - - -
321I LEU* 3.7 5.2 - - + +
322I GLN 3.3 8.1 - - - +
323I LYS* 3.7 23.6 - - + +
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Residues in contact with VAL 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I VAL* 3.9 34.1 - - + -
33I VAL 4.7 0.7 - - - +
34I PHE* 3.9 24.7 - - + -
282I THR* 3.6 21.1 - - + +
283I GLU* 1.3 82.5 - - - +
285I ASP* 1.3 73.0 + - - +
286I LEU* 3.5 18.5 - - + +
289I PRO* 4.5 1.6 - - + -
321I LEU* 3.3 11.9 - - - +
322I GLN* 2.7 36.3 + - + +
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Residues in contact with ASP 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283I GLU* 4.3 0.6 + - - +
284I VAL* 1.3 75.0 - - - +
286I LEU* 1.3 61.5 + - - +
287I ARG* 3.4 32.7 - - - +
288I LYS* 4.4 6.8 + - - +
289I PRO* 3.3 18.9 - - - +
319I LEU* 4.2 10.9 - - - +
320I ALA 4.0 2.5 - - - -
321I LEU* 3.7 18.2 - - + +
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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