Contacts of the strand formed by residues 371 - 375 (chain A) in PDB entry 1E5E
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 MET 371 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A PRO* 4.4 5.4 - - - -
160A THR* 4.2 13.0 - - + -
288A TYR* 3.8 19.3 - - + -
313A THR* 3.4 24.9 - - + -
314A PHE 3.4 5.8 - - - +
315A ILE* 3.7 26.5 - - + -
348A HIS* 3.3 24.9 + - - -
349A PRO* 3.5 18.9 - - + +
350A ALA 5.4 0.2 + - - -
366A GLY 3.1 27.6 - - - +
367A ILE* 3.9 17.3 - - + -
368A THR* 3.2 20.3 + - + +
369A ASP 3.3 0.2 - - - -
370A GLY* 1.3 77.7 - - - +
372A ILE* 1.3 61.6 + - - +
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Residues in contact with ILE 372 (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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313A THR* 3.4 7.2 - - - +
314A PHE* 2.7 69.7 + - + +
316A LEU* 3.8 20.4 - - + -
323A ALA* 3.7 31.2 - - + -
326A LEU* 4.0 0.9 - - + -
327A LEU* 3.9 18.4 - - + -
346A ILE* 3.5 35.4 - - + -
347A GLN 3.6 7.4 - - - +
348A HIS* 5.0 0.4 - - + -
349A PRO* 4.3 1.1 - - - -
370A GLY 4.1 2.5 - - - +
371A MET* 1.3 78.1 - - - +
373A ARG* 1.3 62.1 + - - +
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Residues in contact with ARG 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASN* 3.0 28.7 + - - +
159A PRO* 3.9 11.4 - - + +
161A LEU* 5.8 0.2 - - + -
187A PHE* 4.4 2.7 - - + -
311A MET* 3.7 24.7 - - + +
312A ILE 4.0 2.0 - - - +
313A THR* 3.6 18.4 - - + +
338A SER 3.3 19.2 + - - +
339A LEU* 3.9 9.9 - - - +
345A LEU 4.1 0.3 - - - +
346A ILE* 3.3 5.5 - - - +
347A GLN* 2.9 76.7 + - - +
349A PRO* 3.9 9.3 - - + +
353A THR* 4.1 2.0 + - - +
372A ILE* 1.3 74.4 - - - +
374A LEU* 1.3 62.1 + - - +
375A SER* 6.0 0.2 - - - -
405A PPJ 2.7 43.6 + - - -
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A VAL* 3.9 10.3 - - + -
278A LEU* 4.5 5.2 - - + -
310A SER 3.9 0.3 - - - +
311A MET* 3.4 10.1 - - - +
312A ILE* 2.9 49.2 + - + +
314A PHE* 4.5 6.7 - - + -
333A ILE* 3.8 24.9 - - + -
344A SER* 4.7 3.1 - - - -
345A LEU 3.5 15.5 - - - +
346A ILE* 4.2 8.7 - - + -
373A ARG* 1.3 74.9 - - - +
375A SER* 1.3 65.7 + - - +
376A VAL* 3.8 25.1 - - + -
388A PHE* 3.6 34.3 - - + -
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Residues in contact with SER 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TYR* 3.3 15.2 + - - -
310A SER* 3.8 4.0 + - - -
311A MET* 3.4 7.0 - - - -
338A SER 4.9 0.4 - - - -
339A LEU* 3.6 27.1 - - - -
340A GLY* 2.9 23.9 + - - -
341A GLY 4.7 0.7 + - - -
343A GLU 4.5 1.3 - - - +
344A SER* 3.3 4.7 - - - -
345A LEU* 2.8 41.2 + - - +
374A LEU* 1.3 74.6 - - - +
376A VAL* 1.3 60.2 + - - +
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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