Contacts of the strand formed by residues 358 - 362 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ALA* 3.8 17.7 - - + -
203D SER 3.8 15.0 - - - +
204D CYS* 4.5 4.9 - - - -
205D TYR 3.6 31.9 - - - +
206D SER* 3.5 4.8 - - - +
231D HIS* 3.6 32.1 - - + -
335D CYS* 4.3 0.4 - - - -
354D SER* 2.8 23.0 + - - -
356D ASN* 2.7 26.3 + - - +
357D HIS* 1.3 82.2 - - + +
359D ILE* 1.3 73.2 + - - +
360D LEU* 6.2 0.2 - - + -
402D ARG* 4.1 7.2 - - + -
403D LEU 3.1 13.5 - - - +
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Residues in contact with ILE 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D SER* 4.6 4.9 - - - -
335D CYS* 3.6 20.0 - - - -
338D LEU* 4.3 10.1 - - + -
339D SER* 4.0 25.6 - - - +
342D LEU* 3.9 27.6 - - + -
349D ILE* 4.1 23.6 - - + -
353D GLY 4.8 0.2 - - - +
354D SER* 3.6 11.2 - - - -
358D LEU* 1.3 87.4 - - - +
360D LEU* 1.3 61.8 + - - +
361D MSE 5.0 0.9 - - + -
401D LEU 3.6 0.7 - - - +
402D ARG* 3.6 6.1 - - - +
403D LEU* 3.0 48.7 + - + +
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Residues in contact with LEU 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D CYS* 3.9 19.3 - - - +
206D SER* 5.4 2.7 - - - -
349D ILE* 3.6 7.6 - - - +
350D VAL* 3.0 53.9 + - + +
358D LEU* 6.2 0.4 - - + -
359D ILE* 1.3 75.0 - - - +
361D MSE 1.3 62.2 + - - +
387D ASN* 3.8 27.6 - - + +
388D THR 3.5 27.1 - - - +
389D CYS* 3.9 8.3 - - - -
390D PRO* 4.4 7.6 - - + -
400D GLY* 4.4 2.2 - - - -
401D LEU 3.4 21.8 - - - +
402D ARG 4.4 0.4 - - - +
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Residues in contact with MSE 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D LEU* 4.0 23.8 - - + -
347D TYR* 4.7 11.2 - - + -
348D LYS 3.4 5.2 - - - +
349D ILE* 3.6 20.9 - - + -
359D ILE* 5.0 1.3 - - + -
360D LEU* 1.3 72.0 - - - +
362D ASP* 1.3 54.8 + - - +
363D LEU* 3.5 19.4 + - + -
384D CYS* 5.7 0.4 - - - -
389D CYS* 4.1 3.4 - - - -
399D SER 3.3 0.2 - - - +
400D GLY* 2.7 36.2 - - - -
401D LEU* 2.9 48.9 + - + +
403D LEU* 3.4 30.3 - - + -
425D ILE* 4.3 15.0 - - + -
429D ILE* 4.4 10.5 - - + -
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Residues in contact with ASP 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D TYR* 6.1 0.4 - - - -
348D LYS* 2.9 56.4 + - + +
350D VAL* 4.7 4.9 - - + -
360D LEU 3.9 0.6 + - - -
361D MSE 1.3 68.8 - - - +
363D LEU* 1.3 59.1 + - - +
364D ARG* 3.0 62.5 + - - +
365D SER* 3.5 19.4 + - - -
366D LYS* 5.7 0.2 - - - +
389D CYS* 3.6 16.1 - - - -
399D SER* 3.3 7.5 - - - +
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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