Contacts of the strand formed by residues 337 - 340 (chain C) in PDB entry 4EEM
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A PRO* 3.2 28.5 - - + +
253C PRO* 3.8 1.9 - - - +
254C MET* 2.9 60.6 + - + +
255C ASN* 4.2 3.0 + - - -
258C ASN* 5.1 0.2 + - - -
272C ALA* 3.4 13.4 - - - +
278C PHE* 4.4 14.8 - - + +
333C ALA 3.1 16.9 + - - -
334C VAL 3.2 11.8 + - - -
335C VAL 3.2 3.3 - - - +
336C GLY* 1.3 77.1 - - - +
338C THR* 1.3 64.1 + - - +
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Residues in contact with THR 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C LEU* 4.0 22.0 - - + -
252C ILE 3.4 26.7 - - - +
253C PRO* 4.3 5.8 - - + +
254C MET* 4.5 1.3 - - - +
258C ASN* 4.5 2.1 + - - -
260C TYR* 5.6 1.3 - - - +
269C ILE 4.3 1.6 + - - -
270C SER* 3.6 19.2 - - - -
272C ALA 2.9 8.7 + - - +
273C MET* 3.3 17.5 - - + -
274C ASP* 2.9 26.9 + - - +
278C PHE* 5.2 0.2 - - - -
289C VAL* 5.4 1.3 - - + -
336C GLY 3.1 15.6 + - - -
337C THR* 1.3 75.9 + - - +
339C ARG* 1.3 69.1 + - - +
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Residues in contact with ARG 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 6.1 0.9 - - - -
406A SO4 4.9 9.6 + - - -
143C ILE* 3.2 30.0 + - + -
144C GLU* 4.3 5.5 + - - -
145C PHE* 3.5 30.8 - - + -
250C ASP 3.5 1.4 - - - +
251C LEU* 3.4 3.5 - - - -
252C ILE* 2.7 45.4 + - - +
254C MET* 3.4 32.8 - - + -
274C ASP* 3.4 21.9 + - + +
278C PHE* 6.1 0.7 - - + -
337C THR* 5.8 0.2 - - + -
338C THR* 1.3 76.6 - - - +
340C HIS* 1.3 62.2 + - - +
341C ILE 4.0 0.3 + - - -
342C ARG 6.0 0.4 - - - +
406C SO4 2.7 41.2 + - - -
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Residues in contact with HIS 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C PHE* 4.2 6.0 - - - -
250C ASP* 3.2 21.0 + - - -
251C LEU* 3.8 15.3 - - + -
273C MET* 4.6 1.1 - - + -
274C ASP* 3.2 24.3 + - - +
275C LYS* 3.7 36.2 + - + +
339C ARG* 1.3 75.1 + - - +
341C ILE* 1.3 80.9 + - - +
342C ARG* 3.0 29.2 + - - +
343C HIS* 3.2 11.1 + + - -
403C UDP 3.3 3.9 + - - -
404C MN 2.5 34.3 + - - -
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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