Contacts of the strand formed by residues 246 - 251 (chain I) in PDB entry 5GJQ
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 246 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I LYS* 3.7 27.8 - - - +
176I VAL 5.5 0.2 - - - -
177I GLU* 5.4 4.7 - - - +
244I SER 4.4 0.2 + - - -
245I ALA* 1.3 69.3 - - - +
247I PHE* 1.3 56.6 + - - +
248I LEU* 3.9 2.5 - - - +
277I HIS* 3.6 34.5 - - + +
279I PRO 3.7 2.0 + - - +
280I SER* 2.2 40.4 - - - -
281I ILE 2.7 33.1 + - - -
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Residues in contact with PHE 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I MET 3.4 1.3 - - - +
175I LYS* 3.7 1.8 - - - +
176I VAL* 3.0 46.7 + - + +
177I GLU* 5.5 0.4 + - - -
236I ALA* 3.3 31.4 - - + -
239I VAL* 5.3 1.1 - - + -
240I ALA* 4.2 19.1 - - + -
243I THR* 5.3 2.0 - - + -
245I ALA 3.2 6.1 + - - +
246I THR* 1.3 71.0 - - - +
248I LEU* 1.3 61.2 + - - +
249I ARG* 3.6 5.0 + - + -
281I ILE* 3.1 50.7 - - + -
283I PHE* 4.0 21.1 - + + -
328I ILE* 4.7 2.9 - - + -
283J PHE* 3.1 42.8 - + - -
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Residues in contact with LEU 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I MET* 2.8 39.5 - - + +
175I LYS* 4.1 14.6 - - + -
246I THR* 3.7 4.2 + - - +
247I PHE* 1.3 68.1 - - - +
249I ARG* 1.3 59.9 + - - +
250I VAL 3.5 3.8 + - - -
270I LEU* 3.2 30.9 - - + +
273I VAL* 4.0 17.3 - - + -
274I ALA* 3.1 42.8 - - + +
277I HIS* 4.9 2.0 - - + -
280I SER* 4.6 7.0 - - - +
281I ILE 2.7 14.3 + - - +
282I VAL* 3.7 4.6 - - + -
283I PHE* 2.9 27.1 + - - +
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Residues in contact with ARG 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173I VAL 5.2 0.6 - - - +
174I MET* 3.1 14.9 + - - -
176I VAL* 3.9 13.0 - - + -
233I THR* 5.9 3.2 - - - +
247I PHE* 3.6 3.2 + - + -
248I LEU* 1.3 69.7 - - - +
250I VAL* 1.3 57.3 + - - +
251I VAL* 4.0 17.5 - - - +
283I PHE* 4.0 19.5 - - + -
285I ASP* 4.8 10.7 + - + +
232J ARG* 2.7 50.1 + - - +
275J GLU 4.7 1.3 + - - -
278J ASN* 2.7 63.8 + - - +
279J GLN* 3.6 15.6 - - - +
283J PHE* 3.5 48.5 + - + -
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Residues in contact with VAL 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I MET* 3.6 27.6 - - + -
248I LEU 3.5 0.2 + - - -
249I ARG* 1.3 77.1 - - - +
251I VAL* 1.3 65.0 + - - +
254I GLU* 3.8 5.6 - - + +
255I LEU* 3.6 31.0 - - + -
266I LEU* 6.1 1.6 - - + -
270I LEU* 2.8 49.8 - - + -
283I PHE 3.0 22.7 + - - +
284I ILE* 3.3 19.5 - - + +
285I ASP* 3.8 1.7 + - - -
230J MET* 5.0 3.8 - - + -
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Residues in contact with VAL 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249I ARG* 4.0 30.1 - - - +
250I VAL* 1.3 82.7 - - - +
252I GLY* 1.3 66.3 + - - +
253I SER* 3.4 27.6 - - - +
254I GLU* 2.6 40.2 + - + +
255I LEU 3.1 13.2 + - - -
285I ASP* 3.9 21.5 - - + +
286I GLU* 4.8 8.1 - - + +
232J ARG* 4.8 0.4 - - - +
275J GLU* 4.2 11.2 - - + -
278J ASN* 4.8 7.4 - - - +
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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
------------------------------------------------------------
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