Contacts of the strand formed by residues 358 - 362 (chain C) in PDB entry 1EJI
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 LEU 358 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ALA* 3.9 16.4 - - + -
203C SER 3.8 22.9 - - - +
204C CYS* 4.4 5.4 - - - -
205C TYR 3.6 31.2 - - - +
206C SER* 3.5 5.1 - - - +
231C HIS* 3.9 9.6 - - + -
335C CYS* 4.3 0.4 - - - -
354C SER* 2.7 27.5 + - - -
356C ASN* 2.7 25.9 + - - +
357C HIS* 1.3 97.7 - - + +
359C ILE* 1.3 72.5 + - - +
360C LEU* 6.2 0.2 - - + -
402C ARG* 4.3 7.9 - - + -
403C LEU 3.1 14.4 - - - +
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Residues in contact with ILE 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C SER* 4.6 4.7 - - - -
335C CYS* 3.6 20.6 - - - -
338C LEU* 4.3 10.1 - - + -
339C SER* 4.0 25.8 - - - +
342C LEU* 3.9 27.8 - - + -
349C ILE* 4.2 23.6 - - + -
353C GLY 4.8 0.2 - - - -
354C SER* 3.6 10.8 - - - -
358C LEU* 1.3 87.6 - - - +
360C LEU* 1.3 60.6 + - - +
361C MSE 5.0 0.7 - - + -
401C LEU 3.6 1.0 - - - +
402C ARG* 3.6 5.9 - - - +
403C LEU* 3.0 49.2 + - + +
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Residues in contact with LEU 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C CYS* 3.9 28.0 - - - +
206C SER* 5.4 3.3 - - - -
349C ILE* 3.6 7.7 - - - +
350C VAL* 3.0 46.4 + - + +
358C LEU* 6.2 0.4 - - + -
359C ILE* 1.3 75.0 - - - +
361C MSE 1.3 63.4 + - - +
387C ASN* 3.6 34.8 - - + +
388C THR 4.2 3.4 - - - +
389C CYS* 3.6 31.9 - - + -
390C PRO* 4.5 5.2 - - + -
400C GLY 4.4 0.7 - - - -
401C LEU 3.4 18.2 - - - +
402C ARG* 4.4 0.7 - - - +
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Residues in contact with MSE 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LEU* 4.1 21.3 - - + -
347C TYR* 4.7 11.9 - - + -
348C LYS 3.4 4.9 - - - +
349C ILE* 3.7 21.1 - - + -
350C VAL* 5.1 0.2 - - - -
359C ILE* 5.0 1.1 - - + -
360C LEU* 1.3 74.8 - - - +
362C ASP* 1.3 55.6 + - - +
363C LEU* 3.5 19.8 + - + -
389C CYS* 4.6 0.2 - - - -
399C SER 3.1 0.2 - - - +
400C GLY* 2.7 36.4 - - - -
401C LEU* 3.0 52.3 + - + +
403C LEU* 3.3 31.9 - - + -
425C ILE* 4.3 12.6 - - + -
429C ILE* 4.4 10.3 - - - -
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Residues in contact with ASP 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C TYR* 6.1 0.6 - - - -
348C LYS* 2.9 56.8 + - + +
350C VAL* 4.7 6.7 - - + -
360C LEU 3.9 0.6 + - - -
361C MSE 1.3 69.6 - - - +
363C LEU* 1.3 60.0 + - - +
364C ARG* 3.0 54.3 + - - +
365C SER* 3.5 19.2 + - - -
389C CYS* 3.2 25.9 - - - -
399C SER* 3.2 2.8 - - - +
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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
------------------------------------------------------------
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