Contacts of the strand formed by residues 297 - 301 (chain E) in PDB entry 5IJ7
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 CYS 297 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E SER* 3.6 4.9 - - - -
240E CYS* 3.9 2.9 - - - -
295E VAL* 3.6 3.8 - - - +
296E ASP* 1.3 80.9 + - - +
298E VAL* 1.3 62.5 + - - +
299E ARG* 3.8 15.7 - - - -
307E SER* 3.3 6.9 - - - -
308E LYS* 3.2 32.1 + - + -
352E MET 4.2 3.8 - - - +
353E ARG* 3.7 18.4 - - + -
354E PHE* 3.5 56.8 - - + -
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Residues in contact with VAL 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E SER* 3.3 14.2 + - - +
228E ALA* 3.8 4.5 - - - -
229E ASP* 3.5 4.3 - - + +
238E MET* 3.4 38.8 - - + +
240E CYS* 3.7 23.3 - - + -
246E LEU* 3.6 16.8 - - + -
297E CYS* 1.3 75.0 - - - +
299E ARG* 1.3 92.6 + - - +
305E ILE* 3.6 27.4 - - + -
306E LEU 3.4 4.7 - - - +
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Residues in contact with ARG 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E GLU* 3.2 25.9 + - - -
183E LYS* 3.4 21.6 - - - +
227E SER* 3.6 5.7 + - - -
228E ALA 3.1 22.6 + - - -
229E ASP* 3.4 19.1 - - - +
297E CYS* 3.8 15.3 - - - -
298E VAL* 1.3 99.2 + - - +
300E TRP* 1.3 60.5 + - - +
305E ILE* 3.8 1.5 - - - +
306E LEU* 2.8 34.6 + - - +
353E ARG* 4.5 2.2 - - - +
354E PHE* 3.5 37.8 + - + +
355E SER* 5.2 5.3 - - - +
356E MET* 3.6 24.9 - - + +
401E GLN* 4.5 10.7 - - - +
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Residues in contact with TRP 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E ASP* 2.9 35.6 + - + +
230E TYR 3.2 25.4 - - - +
231E ASP* 3.5 19.8 - - + +
232E LEU* 5.3 1.1 - - + +
236E LYS* 3.4 42.3 + - + -
238E MET* 3.7 29.8 - - + +
248E LEU* 3.5 23.3 - - + -
299E ARG* 1.3 74.2 - - - +
301E LEU* 1.3 52.1 + - - +
302E GLY 3.6 20.2 - - - +
303E ASP 3.8 12.6 - - - -
304E LEU 3.5 20.2 - - - -
305E ILE* 3.8 20.2 - - + +
326E ILE* 4.2 7.2 - - + -
356E MET* 3.3 6.5 - - - +
360E GLN* 2.8 25.1 + - - +
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Residues in contact with LEU 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 4.0 28.9 - - + -
45A ASN* 2.8 19.3 + - - +
46A ARG* 4.3 4.9 - - - +
49A ILE* 3.9 16.4 - - + -
299E ARG 3.7 1.0 + - - -
300E TRP* 1.3 71.2 - - - +
302E GLY* 1.3 58.0 + - - +
304E LEU* 2.9 30.0 + - + +
306E LEU* 3.9 33.2 - - + -
316E CYS* 4.5 4.3 - - - -
342E PHE* 5.8 0.9 - - + -
356E MET* 3.9 10.1 - - - -
360E GLN* 3.6 15.7 - - - +
377E LEU* 3.7 37.2 - - + +
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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