Contacts of the strand formed by residues 348 - 355 (chain A) in PDB entry 4E52
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 LYS 348 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A VAL* 4.0 28.2 - - + +
252A LYS* 3.4 9.4 - - - -
253A PRO* 4.0 27.8 - - + -
346A GLY 4.6 2.5 - - - +
347A GLU* 1.3 76.5 + - - +
349A ARG* 1.3 84.7 + - - +
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Residues in contact with ARG 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A VAL* 3.6 8.1 - - - -
252A LYS 3.0 27.2 + - - +
289A GLU* 5.9 0.4 - - - -
290A ALA* 3.6 22.2 - - - +
292A PHE* 3.5 46.5 - - + +
333A GLU* 2.7 29.4 + - + +
343A ARG* 3.3 41.4 - - + +
347A GLU* 3.8 21.7 + - + +
348A LYS* 1.3 101.3 + - - +
350A LEU* 1.3 65.4 + - - +
351A VAL* 3.4 2.1 + - - +
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A THR* 3.4 26.2 - - - +
249A GLY 4.0 5.2 - - - -
250A PHE 3.7 28.9 - - - +
251A VAL* 3.6 7.2 - - + +
283A LEU 4.5 6.3 - - - +
284A VAL* 4.6 3.6 - - - -
287A LYS* 3.9 29.4 - - + -
289A GLU* 3.7 28.7 - - + +
290A ALA 2.9 20.2 + - - +
291A ALA* 3.4 9.8 - - + +
292A PHE* 3.3 21.5 + - - +
349A ARG* 1.3 73.2 - - - +
351A VAL* 1.3 59.4 + - - +
352A VAL* 3.6 16.7 + - + -
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A THR* 3.0 6.1 + - - -
248A ALA* 2.9 36.7 + - + -
250A PHE* 3.1 22.8 + - + +
252A LYS* 3.7 36.3 - - + +
257A ALA* 3.9 33.2 - - + +
260A LEU* 4.4 7.0 - - + -
261A CYS* 4.3 1.6 - - - -
268A LEU* 4.7 1.6 - - + -
349A ARG 4.0 0.4 - - - +
350A LEU* 1.3 71.6 - - - +
352A VAL* 1.3 62.3 + - - +
353A CYS* 4.3 6.3 - - - -
234C PHE* 4.3 20.0 - - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PHE* 4.2 3.4 - - + -
246A LYS 3.5 16.8 - - - +
247A THR* 3.8 6.5 - - - -
261A CYS* 4.2 0.2 - - - -
268A LEU* 3.7 11.4 - - - +
269A ALA* 3.0 26.3 + - + +
280A LEU* 3.5 29.8 - - + -
283A LEU* 4.1 14.8 - - + -
284A VAL* 5.3 0.4 - - + -
291A ALA* 3.8 16.6 - - + +
292A PHE 4.6 2.1 + - - +
350A LEU* 3.6 28.1 + - + -
351A VAL* 1.3 79.8 - - - +
353A CYS* 1.3 69.4 + - - +
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Residues in contact with CYS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ILE 3.8 0.2 - - - +
245A PHE* 3.3 4.1 - - - -
246A LYS 2.9 33.7 + - - +
261A CYS* 2.0 52.0 - - + -
267A GLN 3.3 7.2 - - - +
269A ALA 4.4 1.1 - - - -
351A VAL* 4.3 1.8 - - - -
352A VAL* 1.3 77.9 - - - +
354A GLU* 1.3 61.7 + - - +
355A PHE* 3.7 23.0 - - + -
234C PHE* 3.2 31.2 - - - -
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LYS* 2.9 40.9 + - + +
244A ILE 3.1 6.1 - - - +
245A PHE* 3.6 17.2 - - + -
266A GLY* 3.4 6.4 - - - -
267A GLN* 2.8 57.0 + - + +
268A LEU 3.7 4.3 - - - +
269A ALA* 4.4 0.4 - - - -
270A SER* 2.7 33.5 + - - -
353A CYS* 1.3 73.9 - - - +
355A PHE* 1.3 63.2 + - - +
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Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A GLU 4.2 0.2 - - - +
243A LYS* 3.7 9.5 - - - +
244A ILE* 2.8 35.8 + - + +
246A LYS* 4.4 11.0 - - + -
264A ALA* 3.5 27.1 - - + -
265A GLY 4.3 2.7 - - - -
266A GLY* 3.9 22.9 - - - -
353A CYS* 3.7 30.7 - - + -
354A GLU* 1.3 74.9 - - - +
227C GLN* 2.9 34.1 + - + +
230C LYS* 3.9 31.1 + - + +
231C VAL* 3.9 31.2 - - + -
234C PHE* 3.8 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