Contacts of the strand formed by residues 337 - 340 (chain B) in PDB entry 4EE5
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 337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B PRO* 3.9 1.4 - - - +
254B MET* 2.9 62.0 + - + +
255B ASN* 4.3 2.3 + - - -
258B ASN* 5.2 0.2 + - - -
272B ALA* 3.2 13.3 + - - +
278B PHE* 4.3 6.9 - - + -
333B ALA 3.2 15.1 + - - -
334B VAL 3.4 10.2 + - - -
335B VAL 3.2 3.2 - - - +
336B GLY* 1.3 77.6 - - - +
338B THR* 1.3 61.0 + - - +
135C PRO* 3.3 26.8 - - - +
136C LEU* 4.2 11.2 - - + -
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Residues in contact with THR 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 4.0 19.5 - - + -
252B ILE 3.3 22.9 - - - +
253B PRO* 4.3 5.6 - - + +
254B MET* 3.9 6.6 - - - +
258B ASN* 4.6 2.9 + - - -
260B TYR* 5.7 1.1 + - - +
269B ILE* 4.5 1.0 + - - +
270B SER* 3.7 17.9 - - - -
272B ALA 2.8 6.5 + - - +
273B MET* 3.3 18.0 - - + -
274B ASP* 3.0 27.5 + - - +
289B VAL* 5.4 1.6 - - + -
336B GLY 3.0 15.7 + - - -
337B THR* 1.3 74.5 + - - +
339B ARG* 1.3 70.3 + - - +
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Residues in contact with ARG 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 3.0 37.3 + - + -
144B GLU* 4.8 0.4 - - - +
145B PHE* 3.5 32.3 - - + -
250B ASP 3.5 1.0 - - - +
251B LEU* 3.4 3.9 - - - -
252B ILE* 2.8 44.0 + - - +
254B MET* 3.3 31.6 - - + +
274B ASP* 3.4 18.3 + - + +
338B THR* 1.3 74.5 - - - +
340B HIS* 1.3 65.2 + - - +
342B ARG* 4.4 10.3 - - - +
408B SO4 2.7 43.0 + - - -
408C SO4 4.7 11.9 + - - -
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Residues in contact with HIS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 3.9 7.3 - - - -
250B ASP* 3.2 25.2 + - - -
251B LEU* 3.6 14.1 - - + -
273B MET* 4.5 1.1 - - + +
274B ASP* 3.1 25.2 + - - +
275B LYS* 3.6 37.3 - - + +
338B THR 4.0 0.2 + - - -
339B ARG* 1.3 76.8 + - - +
341B ILE* 1.3 81.9 + - - +
342B ARG* 3.3 14.5 + - - +
343B HIS* 3.3 10.4 + + - -
404B UDP 3.1 5.4 + - - -
405B MN 2.2 35.4 + - - -
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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
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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